Form990
Click to see attachment
Department of the Treasury
Internal Revenue Service
Return of Organization Exempt From Income Tax
Under section 501(c), 527, or 4947(a)(1) of the Internal Revenue Code (except black lung benefit trust or private foundation)

MediumBullet The organization may have to use a copy of this return to satisfy state reporting requirements.
OMB No. 1545-0047
2011
Open to Public Inspection
A For the calendar year, or tax year beginning 07-01-2011 and ending 06-30-2012
BCheck if applicable:
CName of organization
The Salk Institute for Biological Studies
 
Doing Business As
 
 
Number and street (or P.O. box if mail is not delivered to street address)
10010 N TORREY PINES ROAD
 
Room/suite
City or town, state or country, and ZIP + 4
La Jolla, CA920371002
D Employer identification number

95-2160097
E Telephone number

G Gross receipts $ 172,696,302
F Name and address of principal officer:
WILLIAM BRODY
10010 N TORREY PINES ROAD
LA JOLLA,CA920371002
I
Tax-exempt status: (   ) LeftBullet (insert no.) or
J
Website:MediumBullet
WWW.SALK.EDU
H(a)
Is this a group return for
affiliates?
H(b)
Are all affiliates included?
If "No," attach a list. (see instructions)
H(c)
Group exemption number MediumBullet  
K Form of organization:
 
L Year of formation: 1960
M State of legal domicile: CA
Part I
Summary
Activities & Governance 1 Briefly describe the organization’s mission or most significant activities: BASIC RESEARCH IN THE FOLLOWING: MOLECULAR BIOLOGY & GENETICS, NEUROSCIENCE, AND PLANT BIOLOGY.
2 Check this box MediumBullet
3 Number of voting members of the governing body (Part VI, line 1a)..... 3 29
4 Number of independent voting members of the governing body (Part VI, line 1b) .... 4 25
5 Total number of individuals employed in calendar year 2011 (Part V, line 2a) ... 5 1,039
6 Total number of volunteers (estimate if necessary) .... 6 100
7a Total unrelated business revenue from Part VIII, column (C), line 12 .. 7a -1,127
b Net unrelated business taxable income from Form 990-T, line 34 .. 7b -11,376
Revenues; Prior Year Current Year
8 Contributions and grants (Part VIII, line 1h) ......... 120,830,531 141,948,095
9 Program service revenue (Part VIII, line 2g) ......... 0 0
10 Investment income (Part VIII, column (A), lines 3, 4, and 7d ) .... 4,885,274 4,142,804
11 Other revenue (Part VIII, column (A), lines 5, 6d, 8c, 9c, 10c, and 11e) 2,055,609 3,114,622
12 Total revenue—add lines 8 through 11 (must equal Part VIII, column (A), line 12)................... 127,771,414 149,205,521
Expenses; 13 Grants and similar amounts paid (Part IX, column (A), lines 1–3 )... 0 0
14 Benefits paid to or for members (Part IX, column (A), line 4)..... 0 0
15 Salaries, other compensation, employee benefits (Part IX, column (A), lines 5–10) 64,525,936 67,662,745
16a Professional fundraising fees (Part IX, column (A), line 11e)..... 0 0
b Total fundraising expenses (Part IX, column (D), line 25) MediumBullet4,297,991    
17 Other expenses (Part IX, column (A), lines 11a–11d, 11f–24f).... 46,459,416 52,389,275
18 Total expenses. Add lines 13–17 (must equal Part IX, column (A), line 25) 110,985,352 120,052,020
19 Revenue less expenses. Subtract line 18 from line 12....... 16,786,062 29,153,501
Net Assets or Fund Balances; Beginning of Current Year End of Year
20 Total assets (Part X, line 16)............. 344,678,120 357,920,584
21 Total liabilities (Part X, line 26)............. 109,026,302 101,386,107
22 Net assets or fund balances. Subtract line 21 from line 20..... 235,651,818 256,534,477
Part II
Signature Block
Under penalties of perjury, I declare that I have examined this return, including accompanying schedules and statements, and to the best of my knowledge and belief, it is true, correct, and complete. Declaration of preparer (other than officer) is based on all information of which preparer has any knowledge.
Sign Here
JumboBullet
Signature of officer Date
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Type or print name and title.
Paid preparer use only
Print/type preparer's name
 
Preparer's signature
Date
PTIN
Firm's name Right pointing arrowhead image

Firm's EIN Right pointing arrowhead image
Firm's address Right pointing arrowhead image



Phone no.
May the IRS discuss this return with the preparer shown above? See instructions .........bullet
For Paperwork Reduction Act Notice, see the separate instructions.
Cat. No. 11282Y
Form 990 (2011)
Form 990 (2011)
Page 2
Part III
Statement of Program Service Accomplishments
Check if Schedule O contains a response to any question in this Part III .........
1
Briefly describe the organization’s mission: INVOLVED IN RESEARCH ACTIVITIES, THE OBJECTIVES OF WHICH ARE THE ADVANCEMENT AND DISSEMINATION OF KNOWLEDGE RELEVANT TO THE HEALTH AND WELLBEING OF MAN. THE OBJECTIVES ARE MET PRIMARILY THROUGH RESEARCH AND ADVANCED INSTRUCTION IN (A) BIOLOGY, (B) THE CAUSE, PREVENTION AND CURE OF DISEASES, AND (C) THE FACTORS AND CIRCUMSTANCES CONDUCIVE TO THE FULFILLMENT OF MAN'S BIOLOGICAL POTENTIAL.
2
Did the organization undertake any significant program services during the year which were not listed on
the prior Form 990 or 990-EZ? ....................
If “Yes,” describe these new services on Schedule O.
3
Did the organization cease conducting, or make significant changes in how it conducts, any program services? ..........................
If “Yes,” describe these changes on Schedule O.
4
Describe the organization’s program service accomplishments for each of its three largest program services, as measured by expenses. Section 501(c)(3) and 501(c)(4) organizations and section 4947(a)(1) trusts are required to report the amount of grants and allocations to others, the total expenses, and revenue, if any, for each program service reported.
4a (Code:   ) (Expenses $ 103,461,164 including grants of $   ) (Revenue $   )
LIST OF ACCOMPLISHMENTS 1. "Unnatural" chemical allows Salk researchers to watch protein action in brain cells: Salk scientists have been able to genetically incorporate "unnatural" amino acids, such as those emitting green fluorescence, into neural stem cells, which then differentiate into brain neurons with the incandescent "tag" intact. This new technique, reported in Stem Cells, may help scientists probe the mysteries of many different kinds of stem cells in humans as well as the cells they produce. This could be a boon to both basic and clinical research, such as helping to speed development of stem cell-based regenerative medicine. 2. Salk researchers near goal of using a patient's own cells to make stem cells: A team of Salk researchers developed an improved technique for generating large numbers of blood cells from a patient's own cells. The new technique, published in the journal Stem Cells, will be immediately useful in further stem cell studies and when perfected, could be used in stem cell therapies for a wide variety of conditions, including cancers and immune ailments. 3. A giant leap for plant biology: Salk investigators in collaboration with an international team of scientists recently reported a major leap forward in plant biology, describing in the journal Science their mapping and early analyses of thousands of protein-to-protein interactions within the cells of the model plant Arabidopsis thaliana. With this one study they managed to double the plant protein interaction data that are available to scientists. These data, along with data from future mapping studies, should enable biologists to make agricultural plants more resistant to drought and diseases, more nutritious and generally more useful to mankind. 4. Discovery of insulin switches in pancreas could lead to new diabetes drugs: Salk researchers have discovered how a hormone turns on a series of molecular switches inside the pancreas that increases production of insulin. Published in the Proceedings of the National Academy of Sciences, the finding raises the possibility that new designer drugs might be able to turn on key molecules in this pathway to help the 80 million Americans who have type 2 diabetes or pre-diabetic insulin resistance. The molecular switches command pancreatic beta islet cells, the cells responsible for insulin, to grow and multiply and tweaking these cells might offer a solution to type 1 diabetes, the form of diabetes caused by destruction of islet cells, and to type 2 diabetes, the form caused by insulin resistance. By understanding how pancreatic cells can be encouraged to produce insulin in the most efficient way possible, those cells may be able to be manipulated to treat or even prevent diabetes. Such new agents might increase the functioning of beta islet cells even in people who have not developed diabetes. 5. The genome guardian's dimmer switch: regulating p53 is a matter of life or death: A team of Salk scientists has shed light on the functioning of an important damage response protein in cells. Although the protein, p53, is known as an important tumor suppressor, it is also critical for determining whether a cell survives stress and continues to function in a variety of situations. The study, which appeared in Genes & Development, shows that a short segment on p53 acts as a dimmer switch that helps control the level of p53 activity in a critical stem cell population and the offspring they generate. One implication of the research is that drugs to lower p53 levels, or to reduce its transcription of other growth-stopping genes, might be used temporarily to reduce unwanted tissue damage from DNA-altering drugs or radiation. Another implication is that p53-boosting drugs, which are currently being tested in cancer patients, could have dangerous side effects if used in combination with other drugs that cause DNA damage. 6. Bionic bacteria may help fight disease and global warming: A strain of genetically enhanced bacteria developed by researchers at the Salk Institute may pave the way for new synthetic drugs and new ways of manufacturing medicines and biofuels, according to a paper published in Nature Chemical Biology. For the first time, the scientists were able to create bacteria capable of effectively incorporating "unnatural" amino acids - artificial additions to the 20 naturally occurring amino acids used as biological building blocks - into proteins at multiple sites. This ability may provide a powerful new tool for the study of biological processes and for engineering bacteria that produce new types of synthetic chemicals. 7. Salk breathes new life into fight against primary killer of premature infants: A discovery by scientists at the Salk Institute might explain why some premature infants fail to respond to existing treatments for a deadly respiratory distress syndrome (RDS) and offers clues for new ways to treat the breathing disorder. RDS affects about one percent of infants born in the United States and is the leading cause of death among premature babies. The findings, published in Nature Medicine, identified a new form of RDS in newborn mice and traced the problem to a cellular receptor for thyroid hormone, a key player in many developmental processes in the body. The research has provided new insight toward explaining and treating RDS and other respiratory problems that occur in infants. 8.Long-lived fruit flies offer Salk scientists clues to slowing human aging and fighting disease: A new study in fruit flies, published online in Cell Metabolism, is helping to explain why minimal diets are linked to longevity and offering clues to the effects of aging on stem cell behavior. Scientists at the Salk Institute and their collaborators found that tweaking a gene known as PGC-1, which is also found in human DNA, in the intestinal stem cells of fruit flies delayed the aging of their intestine and extended their lifespan by as much as 50 percent. The findings suggest that the fruit fly version of PCG-1 can act as a biological dial for slowing the aging process and might serve as a target for drugs or other therapies to put the brakes on aging and age-related diseases. 9. Scientists identify gene crucial to normal development of lungs and brain: Researchers at the Salk Institute have identified a gene that tells cells to develop multiple cilia, tiny hair-like structures that move fluids through the lungs and brain. The findings of the research, published in Nature Cell Biology, may help scientists generate new therapies that use stem cells to replace damaged tissues in the lung and other organs. 10. Discovery of plant proteins may boost agricultural yields and biofuel production: In a collaborative study, scientists at the Salk Institute discovered a family of plant proteins that play a role in the production of seed oils, substances important for animal and human nutrition, bio renewable chemicals and biofuels. Scoring a rare scientific hat trick, the researchers identified three related proteins in Arabidopsis thaliana that regulate the metabolism of fatty acids, chemical components of all cell membranes and vegetable oils. They dubbed these fatty-acid binding proteins FAP1, FAP2 and FAP3. The findings, reported in Nature, may lead to the development of improved crops yielding higher qualities and quantities of oils, helping to address growing demands for food and fuel and the consequent environmental pressures on the world's ecosystems. 11. Salk scientists discover chemotherapy pathway: A recent study by Salk investigators showed exactly how cells sense the possibility that their DNA is damaged as a first step to responding to the failure to divide properly. The study, published in Nature Structural and Molecular Biology, found that if cells take too long to undergo cell division, protective structures at the tips of their chromosomes, known as telomeres, send out a molecular SOS. The findings have dual implications for cancer chemotherapy. First, they show how a class of anti-cancer drugs that slows cell division-known as mitotic inhibitors-kills cells. More significantly, the findings suggest ways to make therapy with those inhibitors more potent. 12. Salk study could offer drug-free intervention to prevent obesity and diabetes Salk scientists have found that regular eating times and extending the daily fasting period may override the adverse health effects of a high-fat diet and prevent obesity, diabetes and liver disease in mice. The study, published in Cell Metabolism, reported that mice limited to eating during an 8-hour period are healthier than mice that eat freely throughout the day, regardless of the quality and content of their diet. The study sought to determine whether obesity and metabolic diseases result from a high-fat diet or from disruption of metabolic cycles. Obesity is a major health challenge, reaching global pandemic proportions. Obesity increases the risk of a number of health conditions inc
4b (Code:   ) (Expenses $   including grants of $   ) (Revenue $   )
4c (Code:   ) (Expenses $   including grants of $   ) (Revenue $   )
4d Other program services (Describe in Schedule O.)
(Expenses $   including grants of $   ) (Revenue $   )
4e Total program service expensesMediumBullet$ 103,461,164
Form 990 (2011)
Form 990 (2011)
Page 3
Part IV
Checklist of Required Schedules
Yes
No
1
Is the organization described in section 501(c)(3) or 4947(a)(1) (other than a private foundation)? If “Yes,” complete Schedule AClick to see attachment.....................
1
Yes
 
2
Is the organization required to complete Schedule B, Schedule of Contributors? Click to see attachment........
2
Yes
 
3
Did the organization engage in direct or indirect political campaign activities on behalf of or in opposition to candidates for public office? If “Yes,” complete Schedule C, Part IClick to see attachment..........
3
 
No
4
Section 501(c)(3) organizations. Did the organization engage in lobbying activities? If “Yes,” complete Schedule C,
Part IIClick to see attachment.........................
4
Yes
 
5
Is the organization a section 501(c)(4), 501(c)(5), or 501(c)(6) organization that receives membership dues, assessments, or similar amounts as defined in Revenue Procedure 98-19? If “Yes,” complete Schedule C, Part IIIClick to see attachment........................
5
 
No
6
Did the organization maintain any donor advised funds or any similar funds or accounts for which donors have the right to provide advice on the distribution or investment of amounts in such funds or accounts? If “Yes,” complete Schedule D, Part IClick to see attachment....................
6
 
No
7
Did the organization receive or hold a conservation easement, including easements to preserve open space,
the environment, historic land areas or historic structures? If “Yes,” complete Schedule D, Part IIClick to see attachment...
7
 
No
8
Did the organization maintain collections of works of art, historical treasures, or other similar assets? If “Yes,” complete Schedule D, Part III Click to see attachment....................
8
 
No
9
Did the organization report an amount in Part X, line 21; serve as a custodian for amounts not listed in Part X; or provide credit counseling, debt management, credit repair, or debt negotiation services? If “Yes,”
complete Schedule D, Part IVClick to see attachment...................
9
 
No
10
Did the organization, directly or through a related organization, hold assets in temporarily restricted endowments, permanent endowments, or quasi-endowments? If “Yes,” complete Schedule D, Part VClick to see attachment
10
Yes
 
11
If the organization’s answer to any of the following questions is ‘Yes,’ then complete Schedule D, Parts VI, VII, VIII, IX, or X as applicable:
a
Did the organization report an amount for land, buildings, and equipment in Part X, line10? If “Yes,” complete Schedule D, Part VI.Click to see attachment
11a
Yes
 
b
Did the organization report an amount for investments—other securities in Part X, line 12 that is 5% or more of its total assets reported in Part X, line 16? If “Yes,” complete Schedule D, Part VII.Click to see attachment
11b
Yes
 
c
Did the organization report an amount for investments—program related in Part X, line 13 that is 5% or more of its total assets reported in Part X, line 16? If “Yes,” complete Schedule D, Part VIII.Click to see attachment
11c
 
No
d
Did the organization report an amount for other assets in Part X, line 15 that is 5% or more of its total assets reported in Part X, line 16? If “Yes,” complete Schedule D, Part IX.Click to see attachment
11d
 
No
e
Did the organization report an amount for other liabilities in Part X, line 25? If “Yes,” complete Schedule D, Part X.Click to see attachment
11e
Yes
 
f
Did the organization’s separate or consolidated financial statements for the tax year include a footnote that addresses the organization’s liability for uncertain tax positions under FIN 48 (ASC 740)? If “Yes,” complete Schedule D, Part X.Click to see attachment
11f
 
No
12a
Did the organization obtain separate, independent audited financial statements for the tax year?
If “Yes,” complete Schedule D, Parts XI, XII, and XIII Click to see attachment
12a
Yes
 
b
Was the organization included in consolidated, independent audited financial statements for the tax year? If “Yes,” and if the organization answered ‘No’ to line 12a, then completing Schedule D, Parts XI, XII, and XIII is optional Click to see attachment
12b
 
No
13
Is the organization a school described in section 170(b)(1)(A)(ii)? If “Yes,” complete Schedule E
13
 
No
14a
Did the organization maintain an office, employees, or agents outside of the United States?....
14a
 
No
b
Did the organization have aggregate revenues or expenses of more than $10,000 from grantmaking, fundraising, business, investment, and program service activities outside the United States or aggregate foreign investments valued at $100,000 or more? If “Yes,” complete Schedule F, Part I......... Click to see attachment
14b
Yes
 
15
Did the organization report on Part IX, column (A), line 3, more than $5,000 of grants or assistance to any organization or entity located outside the U.S.? If “Yes,” complete Schedule F, Part II.. Click to see attachment
15
 
No
16
Did the organization report on Part IX, column (A), line 3, more than $5,000 of aggregate grants or assistance to individuals located outside the U.S.? If “Yes,” complete Schedule F, Part III.. Click to see attachment
16
 
No
17
Did the organization report a total of more than $15,000, of expenses for professional fundraising services on Part IX, column (A), lines 6 and 11e? If “Yes,” complete Schedule G, Part IClick to see attachment
17
 
No
18
Did the organization report more than $15,000 total of fundraising event gross income and contributions on Part VIII, lines 1c and 8a? If “Yes,” complete Schedule G, Part II.......... Click to see attachment
18
Yes
 
19
Did the organization report more than $15,000 of gross income from gaming activities on Part VIII, line 9a? If “Yes,” complete Schedule G, Part III................... Click to see attachment
19
 
No
20a
Did the organization operate one or more hospitals? If “Yes,” complete Schedule H.....
20a
 
No
b
If “Yes” to line 20a, did the organization attach a copy of its audited financial statement to this return? Note. All Form 990 filers that operated one or more hospitals must attach audited financial statements.
20b
 
 
Form 990 (2011)
Form 990 (2011)
Page 4
Part IV
Checklist of Required Schedules (continued)
21
Did the organization report more than $5,000 of grants and other assistance to any government or organization in the United States on Part IX, column (A), line 1? If “Yes,” complete Schedule I, Parts I and II..
21
 
No
22
Did the organization report more than $5,000 of grants and other assistance to individuals in the United States on Part IX, column (A), line 2? If “Yes,” complete Schedule I, Parts I and III.....
22
 
No
23
Did the organization answer “Yes” to Part VII, Section A, questions 3, 4, or 5, about compensation of the organization’s current and former officers, directors, trustees, key employees, and highest compensated employees? If “Yes,” complete Schedule J................ Click to see attachment
23
Yes
 
24a
Did the organization have a tax-exempt bond issue with an outstanding principal amount of more than $100,000 as of the last day of the year, that was issued after December 31, 2002? If “Yes,” answer questions 24b–24d and complete Schedule K. If “No,” go to line 25................ Click to see attachment
24a
Yes
 
b
Did the organization invest any proceeds of tax-exempt bonds beyond a temporary period exception?...
24b
 
No
c
Did the organization maintain an escrow account other than a refunding escrow at any time during the year
to defease any tax-exempt bonds?......................
24c
 
No
d
Did the organization act as an “on behalf of” issuer for bonds outstanding at any time during the year?...
24d
 
No
25a
Section 501(c)(3) and 501(c)(4) organizations. Did the organization engage in an excess benefit transaction with a disqualified person during the year? If “Yes,” complete Schedule L, Part I...... Click to see attachment
25a
 
No
b
Is the organization aware that it engaged in an excess benefit transaction with a disqualified person in a prior year, and that the transaction has not been reported on any of the organization’s prior Forms 990 or 990-EZ? If “Yes,” complete Schedule L, Part I................ Click to see attachment
25b
 
No
26
Was a loan to or by a current or former officer, director, trustee, key employee, highly compensated employee, or disqualified person outstanding as of the end of the organization’s tax year? If “Yes,” complete Schedule L,
Part II......................... Click to see attachment
26
Yes
 
27
Did the organization provide a grant or other assistance to an officer, director, trustee, key employee, substantial contributor or employee thereof, a grant selection committee member, or to a 35% controlled entity or family member of any of these persons? If “Yes,” complete Schedule L, Part III......... Click to see attachment
27
 
No
28
Was the organization a party to a business transaction with one of the following parties? (see Schedule L, Part IV instructions for applicable filing thresholds, conditions, and exceptions):
a
A current or former officer, director, trustee, or key employee? If “Yes,” complete Schedule L, Part IV ......................... Click to see attachment
28a
 
No
b
A family member of a current or former officer, director, trustee, or key employee? If “Yes,”
complete Schedule L, Part IV................... Click to see attachment
28b
 
No
c
An entity of which a current or former officer, director, trustee, or key employee (or a family member thereof) was an officer, director, trustee, or owner? If “Yes,” complete Schedule L, Part IV.. Click to see attachment
28c
 
No
29
Did the organization receive more than $25,000 in non-cash contributions? If “Yes,” complete Schedule MClick to see attachment
29
Yes
 
30
Did the organization receive contributions of art, historical treasures, or other similar assets, or qualified conservation contributions? If “Yes,” complete Schedule M............ Click to see attachment
30
 
No
31
Did the organization liquidate, terminate, or dissolve and cease operations? If “Yes,” complete Schedule N,
Part I...........................
31
 
No
32
Did the organization sell, exchange, dispose of, or transfer more than 25% of its net assets? If “Yes,” complete Schedule N, Part II.......................
32
 
No
33
Did the organization own 100% of an entity disregarded as separate from the organization under Regulations sections 301.7701-2 and 301.7701-3? If “Yes,” complete Schedule R, Part I........ Click to see attachment
33
 
No
34
Was the organization related to any tax-exempt or taxable entity? If “Yes,” complete Schedule R, Parts II, III, IV, and V, line 1..................... Click to see attachment
34
Yes
 
35a
Did the organization have a controlled entity within the meaning of section 512(b)(13)?
35a
Yes
 
b
If ‘Yes’ to line 35a, did the organization receive any payment from or engage in any transaction with a controlled entity within the meaning of section 512(b)(13)? If “Yes,” complete Schedule R, Part V, line 2... Click to see attachment
35b
 
No
36
Section 501(c)(3) organizations. Did the organization make any transfers to an exempt non-charitable related organization? If “Yes,” complete Schedule R, Part V, line 2........... Click to see attachment
36
 
No
37
Did the organization conduct more than 5% of its activities through an entity that is not a related organization and that is treated as a partnership for federal income tax purposes? If “Yes,” complete Schedule R, Part VIClick to see attachment
37
 
No
38
Did the organization complete Schedule O and provide explanations in Schedule O for Part VI, lines 11 and 19? Note. All Form 990 filers are required to complete Schedule O. ............
38
Yes
 
Form 990 (2011)
Form 990 (2011)
Page 5
Part V
Statements Regarding Other IRS Filings and Tax Compliance
Check if Schedule O contains a response to any question in this Part V .........
Yes
No
1a
Enter the number reported in Box 3 of Form 1096. Enter -0- if not applicable. .......
1a
143
b
Enter the number of Forms W-2G included in line 1a. Enter -0- if not applicable.
1b
0
c
Did the organization comply with backup withholding rules for reportable payments to vendors and reportable gaming (gambling) winnings to prize winners? ..................
1c
Yes
 
2a
Enter the number of employees reported on Form W-3, Transmittal of Wage and Tax Statements filed for the calendar year ending with or within the year covered by this return .....................
2a
1,039
b
If at least one is reported on line 2a, did the organization file all required federal employment tax returns?

Note. If the sum of lines 1a and 2a is greater than 250, you may be required to e-file. (see instructions)
2b
Yes
 
3a
Did the organization have unrelated business gross income of $1,000 or more during the year?.............................
3a
Yes
 
b
If “Yes,” has it filed a Form 990-T for this year? If “No,” provide an explanation in Schedule O.....
3b
Yes
 
4a
At any time during the calendar year, did the organization have an interest in, or a signature or other authority over, a financial account in a foreign country (such as a bank account or securities account)?.......................
4a
 
No
b
If "Yes," enter the name of the foreign country: MediumBullet
See instructions for filing requirements for Form TD F 90-22.1, Report of Foreign Bank and Financial Accounts.
5a
Was the organization a party to a prohibited tax shelter transaction at any time during the tax year?..
5a
 
No
b
Did any taxable party notify the organization that it was or is a party to a prohibited tax shelter transaction?
5b
 
No
c
If “Yes” to line 5a or 5b, did the organization file Form 8886-T? ........
5c
 
 
6a
Does the organization have annual gross receipts that are normally greater than $100,000, and did the organization solicit any contributions that were not tax deductible?..........
6a
 
No
b
If “Yes,” did the organization include with every solicitation an express statement that such contributions or gifts were not tax deductible?........................
6b
 
 
7
Organizations that may receive deductible contributions under section 170(c).
a
Did the organization receive a payment in excess of $75 made partly as a contribution and partly for goods and services provided to the payor?....................
7a
Yes
 
b
If “Yes,” did the organization notify the donor of the value of the goods or services provided?.....
7b
Yes
 
c
Did the organization sell, exchange, or otherwise dispose of tangible personal property for which it was required to file Form 8282?...........................
7c
 
No
d
If “Yes,” indicate the number of Forms 8282 filed during the year ....
7d
 
e
Did the organization receive any funds, directly or indirectly, to pay premiums on a personal benefit contract?..........................
7e
 
No
f
Did the organization, during the year, pay premiums, directly or indirectly, on a personal benefit contract?..
7f
 
No
g
If the organization received a contribution of qualified intellectual property, did the organization file Form 8899 as required?...................
7g
 
 
h
If the organization received a contribution of cars, boats, airplanes, or other vehicles, did the organization file a Form 1098-C?...............
7h
 
 
8
Sponsoring organizations maintaining donor advised funds and section 509(a)(3) supporting organizations. Did the supporting organization, or a donor advised fund maintained by a sponsoring organization, have excess business holdings at any time during the year?................
8
 
 
9
Sponsoring organizations maintaining donor advised funds.
a
Did the organization make any taxable distributions under section 4966?.........
9a
 
 
b
Did the organization make a distribution to a donor, donor advisor, or related person?......
9b
 
 
10
Section 501(c)(7) organizations. Enter:
a
Initiation fees and capital contributions included on Part VIII, line 12 ...
10a
 
b
Gross receipts, included on Form 990, Part VIII, line 12, for public use of club facilities
10b
 
11
Section 501(c)(12) organizations. Enter:
a
Gross income from members or shareholders .........
11a
 
b
Gross income from other sources (Do not net amounts due or paid to other sources against amounts due or received from them) ........
11b
 
12a
Section 4947(a)(1) non-exempt charitable trusts. Is the organization filing Form 990 in lieu of Form 1041?
12a
 
 
b
If “Yes,” enter the amount of tax-exempt interest received or accrued during the year.
12b
 
13
Section 501(c)(29) qualified nonprofit health insurance issuers.
a
Is the organization licensed to issue qualified health plans in more than one state?
Note. All 501(c)(29) organizations must list in Schedule O each state in which they are licensed to issue qualified health plans, the amount of reserves required by each state, and the amount of reserves the organization allocated to each state.
13a
 
 
b
Enter the aggregate amount of reserves the organization is required to maintain by the states in which the organization is licensed to issue qualified health plans.
13b
 
c
Enter the aggregate amount of reserves on hand.
13c
 
14a
Did the organization receive any payments for indoor tanning services during the tax year?.....
14a
 
 
b
If "Yes," has it filed a Form 720 to report these payments? If “No,” provide an explanation in Schedule O..
14b
 
 
Form 990 (2011)
Form 990 (2011)
Page 6
Part VI
Governance, Management, and Disclosure For each “Yes” response to lines 2 through 7b below, and for a “No” response to lines 8a, 8b, or 10b below, describe the circumstances, processes, or changes in Schedule O. See instructions.
Check if Schedule O contains a response to any question in this Part VI .........
Section A. Governing Body and Management
Yes
No
1a
Enter the number of voting members of the governing body at the end of the tax year
If the governing body delegated broad authority to an executive committee or similar committee, explain in Schedule O.
1a
29
b
Enter the number of voting members included in line 1a, above, who are independent .................
1b
25
2
Did any officer, director, trustee, or key employee have a family relationship or a business relationship with any other officer, director, trustee, or key employee? .................
2
 
No
3
Did the organization delegate control over management duties customarily performed by or under the direct supervision of officers, directors or trustees, or key employees to a management company or other person? .
3
 
No
4
Did the organization make any significant changes to its governing documents since the prior Form 990 was filed?
4
 
No
5
Did the organization become aware during the year of a significant diversion of the organization’s assets? .
5
 
No
6
Did the organization have members or stockholders? ................
6
Yes
 
7a
Did the organization have members, stockholders, or other persons who had the power to elect or appoint one or more members of the governing body? .................
7a
Yes
 
b
Are any governance decisions of the organization reserved to (or subject to approval by) members, stockholders, or persons other than the governing body? ............
7b
Yes
 
8
Did the organization contemporaneously document the meetings held or written actions undertaken during the year by the following:
a
The governing body? .........................
8a
Yes
 
b
Each committee with authority to act on behalf of the governing body? ..........
8b
Yes
 
9
Is there any officer, director, trustee, or key employee listed in Part VII, Section A, who cannot be reached at the organization’s mailing address? If “Yes,” provide the names and addresses in Schedule O .....
9
 
No
Section B. Policies (This Section B requests information about policies not required by the Internal
Revenue Code.)
Yes
No
10a
Did the organization have local chapters, branches, or affiliates? ............
10a
 
No
b
If “Yes,” did the organization have written policies and procedures governing the activities of such chapters, affiliates, and branches to ensure their operations are consistent with the organization's exempt purposes? ....
10b
 
 
11a
Has the organization provided a complete copy of this Form 990 to all members of its governing body before filing the form?
11a
Yes
 
b
Describe in Schedule O the process, if any, used by the organization to review the Form 990. .....
12a
Did the organization have a written conflict of interest policy? If “No,” go to line 13.......
12a
Yes
 
b
Were officers, directors or trustees, and key employees required to disclose annually interests that could give rise to conflicts? ........................
12b
Yes
 
c
Did the organization regularly and consistently monitor and enforce compliance with the policy? If “Yes,” describe in Schedule O how this was done ....................
12c
Yes
 
13
Did the organization have a written whistleblower policy? ...............
13
Yes
 
14
Did the organization have a written document retention and destruction policy? .........
14
Yes
 
15
Did the process for determining compensation of the following persons include a review and approval by independent persons, comparability data, and contemporaneous substantiation of the deliberation and decision?
a
The organization’s CEO, Executive Director, or top management official ...........
15a
Yes
 
b
Other officers or key employees of the organization ................
15b
Yes
 
If "Yes," to line 15a or 15b, describe the process in Schedule O (see instructions).
16a
Did the organization invest in, contribute assets to, or participate in a joint venture or similar arrangement with a taxable entity during the year? ......................
16a
 
No
b
If “Yes,” did the organization follow a written policy or procedure requiring the organization to evaluate its participation in joint venture arrangements under applicable federal tax law, and take steps to safeguard the organization’s exempt status with respect to such arrangements? ............
16b
 
 
Section C. Disclosure
17
List the States with which a copy of this Form 990 is required to be filedMediumBullet
AL , AK , AZ , AR , CA , CT , GA , HI , IL , KS , KY , ME , MD , MA , MI , MN , MS , NH , NJ , NM , NY , NC , OH , OK , OR , PA , RI , SC , TN , UT , VA , WA , WV , WI
18
Section 6104 requires an organization to make its Form 1023 (or 1024 if applicable), 990, and 990-T (501(c)(3)s only) available for public inspection. Indicate how you made these available. Check all that apply.
19
Describe in Schedule O whether (and if so, how), the organization made its governing documents, conflict of interest policy, and financial statements available to the public during the tax year.
20
State the name, physical address, and telephone number of the person who possesses the books and records of the organization: MediumBullet
KIM E WITMER
10010 N TORREY PINES ROAD
LA JOLLA,CA920371002
(858) 453-4100
Form 990 (2011)
Form 990 (2011)
Page 7
Part VII
Compensation of Officers, Directors,Trustees, Key Employees, Highest Compensated Employees, and Independent Contractors
Check if Schedule O contains a response to any question in this Part VII .........
Section A. Officers, Directors, Trustees, Key Employees, and Highest Compensated Employees
1a Complete this table for all persons required to be listed. Report compensation for the calendar year ending with or within the organization’s tax year.
RoundBullet List all of the organization’s current officers, directors, trustees (whether individuals or organizations), regardless of amount
of compensation, and current key employees. Enter -0- in columns (D), (E), and (F) if no compensation was paid.

RoundBullet List all of the organization’s current key employees, if any. See instructions for definition of "key employee."
RoundBullet List the organization’s five current highest compensated employees (other than an officer, director, trustee or key employee)
who received reportable compensation (Box 5 of Form W-2 and/or Box 7 of Form 1099-MISC) of more than $100,000 from the
organization and any related organizations.

RoundBullet List all of the organization’s former officers, key employees, or highest compensated employees who received more than $100,000
of reportable compensation from the organization and any related organizations.

RoundBullet List all of the organization’s former directors or trustees that received, in the capacity as a former director or trustee of the
organization, more than $10,000 of reportable compensation from the organization and any related organizations.

List persons in the following order: individual trustees or directors; institutional trustees; officers; key employees; highest
compensated employees; and former such persons.
Check this box if neither the organization nor any related organizations compensated any current or former officer, director, or trustee.
(A)
Name and Title 		(B)
Average hours per week (describe hours for related organizations in Schedule O) 		(C)
Position (do not check more than one box, unless person is both an officer and a director/trustee) 		(D)
Reportable compensation from the organization (W- 2/1099-MISC) 		(E)
Reportable compensation from related organizations (W- 2/1099-MISC) 		(F)
Estimated amount of other compensation from the organization and related organizations
Individual Trustee or Director; Institutional Trustee; Officer; Key Employee; Highest compensated employee; Former;
(1) William R Brody MD PhD
President
 50.0 X   X       802,842 0 143,981
(2) Irwin M Jacobs SM ScD
Chair
 3.0 X   X       0 0 0
(3) Darlene M Shiley
Vice Chair
 2.0 X   X       0 0 0
(4) Theodore Waitt
Vice Chair
 2.0 X   X       0 0 0
(5) Thomas D Albright PhD
Trustee/Professor
 50.0 X           233,830 0 46,760
(6) Charles H Brandes
Trustee
 2.0 X           0 0 0
(7) Linda L Chester
Trustee
 .5 X           0 0 0
(8) Frederick J Dotzler
Trustee
 .5 X           0 0 0
(9) Jennifer L Howse PhD
Trustee
 .5 X           0 0 0
(10) Dean Kamen
Trustee
 .5 X           0 0 0
(11) Christoper R Kintner PHD
Trustee/Professor
 50.0 X           203,114 0 31,266
(12) Benjamin H Lewis
Trustee
 .5 X           0 0 0
(13) Corinne Mentzelopoulos
Trustee
 .5 X           0 0 0
(14) Howard H Newman PhD
Trustee
 2.0 X           0 0 0
(15) Ralph S O'Connor
Trustee
 .5 X           0 0 0
(16) Gerald S Parsky
Trustee
 .5 X           0 0 0
(17) Frederik Paulsen PhD
Trustee
 .5 X           0 0 0
Form 990 (2011)
Form 990 (2011)
Page 8
Part VII
Section A. Officers, Directors, Trustees, Key Employees, and Highest Compensated Employees (continued)
(A)
Name and Title 		(B)
Average hours per week (describe hours for related organizations in Schedule O) 		(C)
Position (do not check more than one box, unless person is both an officer and a director/trustee) 		(D)
Reportable compensation from the organization (W- 2/1099-MISC) 		(E)
Reportable compensation from related organizations (W- 2/1099-MISC) 		(F)
Estimated amount of other compensation from the organization and related organizations
Individual Trustee or Director; Institutional Trustee; Officer; Key Employee; Highest compensated employee; Former;
(18) Caryl Philips
Trustee
 .5 X           0 0 0
(19) Conrad T Prebys
Trustee
 .5 X           0 0 0
(20) Ernest S Rady
Trustee
 .5 X           0 0 0
(21) Faye H Russell
Trustee
 .5 X           0 0 0
(22) Mary Jane Salk
Trustee
 .5 X           0 0 0
(23) Benjamin S Schapiro
Trustee
 .5 X           0 0 0
(24) Carla J Shatz PhD
Trustee/Non Resident Fellow
 .5 X           0 0 0
(25) Jerre L Stead
Trustee
 2.0 X           0 0 0
(26) Geoffrey M Wahl PhD
Trustee/Professor
 50.0 X           247,411 0 47,227
(27) Harvey P White
Trustee
 .5 X           0 0 0
(28) Marna C Whittington PhD
Trustee
 .5 X           0 0 0
(29) M Faye Wilson
Trustee
 .5 X           0 0 0
(30) Marsha A Chandler PhD
Exec. Vice Pres/COO
 50.0     X       466,184 0 33,320
(31) Julia A Miller JD
Secretary/Gen. Counsel
 50.0     X       249,696 0 15,664
(32) Kim E Witmer
Treasurer/Sr. VP/CFO
 50.0     X       353,372 0 47,514
(33) Fred H Gage PhD
Professor
 50.0         X   312,204 0 43,981
(34) Rebecca R Newman
VP, Dev. & Inst Relations
 50.0         X   331,730 0 40,226
(35) Dennis D O'Leary PhD
Professor
 50.0         X   306,350 0 47,514
(36) Wylie W Vale PHD
Professor
 50.0         X   332,335 0 43,981
(37) Inder Verma PhD
Professor
 50.0         X   360,446 0 43,981
1b Sub-Total................MediumBullet
c Total from continuation sheets to Part VII, Section A....MediumBullet
d Total (add lines 1b and 1c)............MediumBullet 4,199,514 0 585,415
2
Total number of individuals (including but not limited to those listed above) who received more than $100,000 of reportable compensation from the organizationMediumBullet80
Yes
No
3
Did the organization list any former officer, director or trustee, key employee, or highest compensated employee on line 1a? If “Yes,” complete Schedule J for such individual .............
3
 
No
4
For any individual listed on line 1a, is the sum of reportable compensation and other compensation from the organization and related organizations greater than $150,000? If “Yes,” complete Schedule J for such individual...........................
4
Yes
 
5
Did any person listed on line 1a receive or accrue compensation from any unrelated organization or individual for services rendered to the organization? If “Yes,” complete Schedule J for such person .....
5
 
No
Section B. Independent Contractors
1
Complete this table for your five highest compensated independent contractors that received more than $100,000 of compensation from the organization. Report compensation for the calendar year ending with or within the organization’s tax year.
(A)
Name and business address 		(B)
Description of services 		(C)
Compensation
RUDOLPH SLETTEN INC
10955 VISTA SORRENTO PKWY
SAN DIEGO,CA92130 		General Contractor 18,833,015
UC REGENTS SAN DIEGO
9500 GILMAN DRIVE
LA JOLLA,CA92093 		TRNG PROGRAM/SUBCONT 1,668,963
SAN DIEGO GAS ELECTRIC
PO BOX 129831
SAN DIEGO,CA92112 		FACILITIES & MAINT. 1,070,123
STELLAR SOLAR
6965 EL CAMINO REAL SUITE 105
CARLSBAD,CA92009 		SOLAR ENERGY SYSTEM 1,847,559
SECURITAS SECURITY SERVICE
FILE 57220
LOS ANGELES,CA90074 		SECURITY 506,230
2
Total number of independent contractors (including but not limited to those listed above) who received more than $100,000 of compensation from the organization MediumBullet19
Form 990 (2011)
Form 990 (2011)
Page 9
Part VIII
Statement of Revenue
(A)
Total revenue 		(B)
Related or
exempt
function
revenue 		(C)
Unrelated
business
revenue 		(D)
Revenue
excluded from
tax under sections
512, 513, or 514
Contributions, Gifts, Grants and Other Similar Amounts 1a Federated campaigns..1a  
b Membership dues....1b  
c Fundraising events....1c 580,857
d Related organizations...1d  
e Government grants (contributions)1e 65,788,133
f All other contributions, gifts, grants, and
similar amounts not included above1f 		75,579,105
g Noncash contributions included in lines 1a-1f:$ 3,558,046
h Total. Add lines 1a-1f.......MediumBullet 141,948,095
Program Service Revenue Business Code
2a
b
c
d
e
f All other program service revenue .        
g Total. Add lines 2a–2f........MediumBullet 0
Other Revenue 3 Investment income (including dividends, interest
and other similar amounts).....MediumBullet 1,621,359     1,621,359
4 Income from investment of tax-exempt bond proceeds..MediumBullet 0     0
5 Royalties............MediumBullet 2,785,633     2,785,633
(i) Real (ii) Personal
6a Gross rents    
b Less: rental expenses    
c Rental income or (loss)    
d Net rental income or (loss).......MediumBullet        
(i) Securities (ii) Other
7a Gross amount from sales of assets other than inventory 25,746,293 44,750
b Less: cost or other basis and sales expenses 23,231,106 38,492
c Gain or (loss) 2,515,187 6,258
d Net gain or (loss)..........MediumBullet 2,521,445     2,521,445
8a Gross income from fundraising events (not including
$ 580,857
of contributions reported on line 1c). See Part IV, line 18 ...
a 143,925
b Less: direct expenses ...b 221,183
c Net income or (loss) from fundraising events..MediumBullet -77,258   -77,258
9a Gross income from gaming activities.
See Part IV, line 19 ...
a  
b Less: direct expenses ...b  
c Net income or (loss) from gaming activities...MediumBullet 0      
10a Gross sales of inventory, less
returns and allowances .
a  
b Less: cost of goods sold ..b  
c Net income or (loss) from sales of inventory..MediumBullet 0      
Miscellaneous Revenue Business Code
11a ENERGY REBATE 900,099 400,580     400,580
b OIL ROYALTIES 900,099 6,794     6,794
c UBI(K-1 FLOW THROUGH INCOME) 900,099 -4,163   -4,163  
d All other revenue .... 3,036   3,036  
e Total. Add lines 11a–11d ......MediumBullet 406,247
12 Total revenue. See Instructions....MediumBullet 149,205,521   -1,127 7,258,553
Form 990 (2011)
Form 990 (2011)
Page 10
Part IX
Statement of Functional Expenses
Section 501(c)(3) and 501(c)(4) organizations must complete all columns. All other organizations must complete column (A) but are not required to complete columns (B), (C), and (D).
Check if Schedule O contains a response to any question in this Part IX. .........
Do not include amounts reported on lines 6b,
7b, 8b, 9b, and 10b of Part VIII. 		(A)
Total expenses 		(B)
Program service expenses 		(C)
Management and general expenses 		(D)
Fundraising expenses
1 Grants and other assistance to governments and organizations in the United States. See Part IV, line 21 0  
2 Grants and other assistance to individuals in the United States. See Part IV, line 22 0  
3 Grants and other assistance to governments, organizations, and individuals outside the United States. See Part IV, lines 15 and 16 0  
4 Benefits paid to or for members 0  
5 Compensation of current officers, directors, trustees, and key employees .... 2,984,331 828,212 1,963,685 192,434
6 Compensation not included above, to disqualified persons (as defined under section 4958(f)(1)) and persons described in section 4958(c)(3)(B) .... 699,316 699,316    
7 Other salaries and wages 48,036,614 41,916,570 4,082,290 2,037,754
8 Pension plan accruals and contributions (include section 401(k) and 403(b) employer contributions) .... 4,393,488 3,635,961 562,271 195,256
9 Other employee benefits ....... 8,027,132 6,643,090 1,027,299 356,743
10 Payroll taxes ........... 3,521,864 2,914,623 450,722 156,519
11 Fees for services (non-employees):        
a Management ...... 653,287 101,824 440,283 111,180
b Legal ......... 828,021 784,472 43,549  
c Accounting ........... 213,982   213,982  
d Lobbying ........... 0      
e Professional fundraising. See Part IV, line 17.. 0  
f Investment management fees ...... 204,663   204,663  
g Other .......... 5,512,253 4,941,999 439,097 131,157
12 Advertising and promotion .... 25,467 1,603 1,556 22,308
13 Office expenses ....... 13,872,190 13,361,084 216,761 294,345
14 Information technology ...... 2,868,830 2,441,070 342,297 85,463
15 Royalties .. 0      
16 Occupancy ........... 6,134,020 4,751,611 1,236,316 146,093
17 Travel ............ 912,030 741,628 39,984 130,418
18 Payments of travel or entertainment expenses for any federal, state, or local public officials ...... 0      
19 Conferences, conventions, and meetings .... 1,254,875 868,431 94,877 291,567
20 Interest ........... 621   621  
21 Payments to affiliates ....... 0      
22 Depreciation, depletion, and amortization ..... 10,615,786 9,988,543 484,485 142,758
23 Insurance .............. 148,480   148,480  
24 Other expenses. Itemize expenses not covered above (List miscellaneous expenses in line 24f. If line 24f amount exceeds 10% of line 25, column (A) amount, list line 24f expenses on Schedule O.)
a SCIENTIFIC SUBCONTRACTS 7,291,284 7,291,284    
b REPAIRS & PARTS 1,460,814 1,432,413 23,508 4,893
c UBI TAXES 2,093   2,093  
d OTHER EXPENSES 390,579 117,430 274,046 -897
e
f All other expenses        
25 Total functional expenses. Add lines 1 through 24f 120,052,020 103,461,164 12,292,865 4,297,991
26 Joint costs. Complete this line only if the organization reported in column (B) joint costs from a combined educational campaign and fundraising solicitation. Check here MediumBullet if following SOP 98-2 (ASC 958-720).        
Form 990 (2011)
Form 990 (2011)
Page 11
Part X Balance Sheet
(A)
Beginning of year 		(B)
End of year
Assets 1 Cash—non-interest-bearing .......... 10,968,328 1 12,698,201
2 Savings and temporary cash investments ....... 0 2 0
3 Pledges and grants receivable, net ......... 24,066,906 3 28,220,160
4 Accounts receivable, net ......... 1,367,629 4 922,755
5 Receivables from current and former officers, directors, trustees, key employees, and highest compensated employees. Complete Part II of
Schedule L .......... 148,500 5 148,500
6 Receivables from other disqualified persons (as defined under section 4958(f)(1)) and persons described in section 4958(c)(3)(B). Complete Part II of
Schedule L .......... 0 6 0
7 Notes and loans receivable, net ............. 1,651,234 7 1,608,475
8 Inventories for sale or use .............. 125,109 8 86,205
9 Prepaid expenses and deferred charges ............ 783,427 9 678,625
10a Land, buildings, and equipment: cost or other basis. Complete Part VI of Schedule D 10a 213,870,646
b Less: accumulated depreciation. ..... 10b 126,065,190 84,139,853 10c 87,805,456
11 Investments—publicly traded securities .......... 116,113,310 11 118,874,737
12 Investments—other securities. See Part IV, line 11 ...... 91,784,543 12 100,033,993
13 Investments—program-related. See Part IV, line 11 .. 0 13 0
14 Intangible assets ......... 0 14 0
15 Other assets. See Part IV, line 11 ........... 13,677,781 15 6,843,477
16 Total assets. Add lines 1 through 15 (must equal line 34)... 344,678,120 16 357,920,584
Liabilities 17 Accounts payable and accrued expenses . 19,343,762 17 17,196,676
18 Grants payable .......... 0 18 0
19 Deferred revenue .......... 25,466,282 19 21,168,387
20 Tax-exempt bond liabilities .......... 57,607,080 20 56,129,568
21 Escrow or custodial account liability. Complete Part IV of Schedule D.. 0 21 0
22 Payables to current and former officers, directors, trustees, key
employees, highest compensated employees, and disqualified
persons. Complete Part II of Schedule L.......... 0 22 0
23 Secured mortgages and notes payable to unrelated third parties .. 0 23 0
24 Unsecured notes and loans payable to unrelated third parties .... 0 24 0
25 Other liabilities (including federal income tax, payables to related third parties, and other liabilities not included on lines 17-24). Complete Part X of Schedule D..... 6,609,178 25 6,891,476
26 Total liabilities. Add lines 17 through 25..... 109,026,302 26 101,386,107
Net Assets or Fund Balance Organizations that follow SFAS 117, check here MediumBullet and complete lines 27 through 29, and lines 33 and 34.
27 Unrestricted net assets ..... 80,926,968 27 78,170,627
28 Temporarily restricted net assets ..... 58,620,417 28 63,947,145
29 Permanently restricted net assets ..... 96,104,433 29 114,416,705
Organizations that do not follow SFAS 117, check here MediumBullet and complete lines 30 through 34.
30 Capital stock or trust principal, or current funds .....   30  
31 Paid-in or capital surplus, or land, building or equipment fund .....   31  
32 Retained earnings, endowment, accumulated income, or other funds   32  
33 Total net assets or fund balances ..... 235,651,818 33 256,534,477
34 Total liabilities and net assets/fund balances ..... 344,678,120 34 357,920,584
Form 990 (2011)
Form 990 (2011)
Page 12
Part XI
Reconcilliation of Net Assets
Check if Schedule O contains a response to any question in this Part XI .........
1
Total revenue (must equal Part VIII, column (A), line 12) ...
1
149,205,521
2
Total expenses (must equal Part IX, column (A), line 25) ....
2
120,052,020
3
Revenue less expenses. Subtract line 2 from line 1 ...
3
29,153,501
4
Net assets or fund balances at beginning of year (must equal Part X, line 33, column (A)) ..
4
235,651,818
5
Other changes in net assets or fund balances (explain in Schedule O) ...
5
-8,270,842
6
Net assets or fund balances at end of year. Combine lines 3, 4, and 5 (must equal Part X, line 33, column (B)) ....
6
256,534,477
Part XII
Financial Statements and Reporting
Check if Schedule O contains a response to any question in this Part XII .........
Yes
No
1
Accounting method used to prepare the Form 990:  
If the organization changed its method of accounting from a prior year or checked "Other," explain in
Schedule O.
2a
Were the organization’s financial statements compiled or reviewed by an independent accountant?....
2a
 
No
b
Were the organization’s financial statements audited by an independent accountant?........
2b
Yes
 
c
If “Yes,” to 2a or 2b, does the organization have a committee that assumes responsibility for oversight of the audit, review, or compilation of its financial statements and selection of an independent accountant? If the organization changed either its oversight process or selection process during the tax year, explain in Schedule O. ...........................
2c
Yes
 
d
If “Yes” to line 2a or 2b, check a box below to indicate whether the financial statements for the year were issued on a separate basis, consolidated basis, or both:
3a
As a result of a federal award, was the organization required to undergo an audit or audits as set forth in the Single Audit Act and OMB Circular A-133? ................
3a
Yes
 
b
If “Yes,” did the organization undergo the required audit or audits? If the organization did not undergo the required audit or audits, explain why in Schedule O and describe any steps taken to undergo such audits. ..
3b
Yes
 
Form 990 (2011)
Additional Data


Software ID:  
Software Version:  
Form 990, Special Condition Description:
Special Condition Description
SCHEDULE A
(Form 990 or 990EZ)

Department of the Treasury
Internal Revenue Service
Public Charity Status and Public Support

Complete if the organization is a section 501(c)(3) organization or a section
4947(a)(1) nonexempt charitable trust.
right arrow Attach to Form 990 or Form 990-EZ. right arrow See separate instructions.
OMB No. 1545-0047
2011
Open to Public
Inspection
Name of the organization
The Salk Institute for Biological Studies
 
Employer identification number

95-2160097
Part I
Reason for Public Charity Status (All organizations must complete this part.) See instructions
The organization is not a private foundation because it is: (For lines 1 through 11, check only one box.)
1
2
3
4
5
section 170(b)(1)(A)(iv). (Complete Part II.)
6
7
8
9
receipts from activities related to its exempt functions—subject to certain exceptions, and (2) no more than 331/3% of
its support from gross investment income and unrelated business taxable income (less section 511 tax) from businesses
acquired by the organization after June 30, 1975. See section 509(a)(2). (Complete Part III.)
10
11
e
f
g
(i) a person who directly or indirectly controls, either alone or together with persons described in (ii)
Yes
No
and (iii) below, the governing body of the the supported organization? ................
11g(i)
 
 
(ii) a family member of a person described in (i) above? ......................
11g(ii)
 
 
(iii) a 35% controlled entity of a person described in (i) or (ii) above? ................
11g(iii)
 
 
h
(i)
Name of supported organization 		(ii)
EIN 		(iii)
Type of organization (described on lines 1- 9 above or IRC section (see instructions)) 		(iv)
Is the organization in col. (i) listed in your governing document? 		(v)
Did you notify the organization in col. (i) of your support? 		(vi)
Is the organization in col. (i) organized in the U.S.? 		(vii)
Amount of support?
Yes No Yes No Yes No
Total                  

For Paperwork Reduction Act Notice, see the Instructions for Form 990.
Cat. No. 11285F
Schedule A (Form 990 or 990-EZ) 2011
Schedule A (Form 990 or 990-EZ) 2011
Page 2
Part II
Support Schedule for Organizations Described in IRC 170(b)(1)(A)(iv) and 170(b)(1)(A)(vi)
(Complete only if you checked the box on line 5, 7, or 8 of Part I or if the organization failed to qualify under Part III. If the organization fails to qualify under the tests listed below, please complete Part III.)
Section A. Public Support
Calendar year(or fiscal year beginning in) (a) 2007 (b) 2008 (c) 2009 (d) 2010 (e) 2011 (f) Total
1 Gifts, grants, contributions, and membership fees received. (Do not include any "unusual grants.") .... 102,548,502 87,583,830 114,311,374 120,830,531 141,948,096 567,222,333
2 Tax revenues levied for the organization's benefit and either paid to or expended on its behalf.......            
3 The value of services or facilities furnished by a governmental unit to the organization without charge..            
4 Total. Add lines 1 through 3.. 102,548,502 87,583,830 114,311,374 120,830,531 141,948,096 567,222,333
5 The portion of total contributions by each person (other than a governmental unit or publicly supported organization) included on line 1 that exceeds 2% of the amount shown on line 11, column (f)..           14,008,590
6 Public Support. Subtract line 5 from line 4.           553,213,743
Section B. Total Support
Calendar year(or fiscal year beginning in) (a) 2007 (b) 2008 (c) 2009 (d) 2010 (e) 2011 (f) Total
7 Amounts from line 4.. 102,548,502 87,583,830 114,311,374 120,830,531 141,948,096 567,222,333
8 Gross income from interest, dividends, payments received on securities loans, rents, royalties and income from similar sources.. 1,297,051 2,714,020 3,494,564 3,483,205 4,407,819 15,396,659
9 Net income from unrelated business activities, whether or not the business is regularly carried on.. 105,259   44,457     149,716
10 Other income. (Explain in Part IV.) Do not include gain or loss from the sale of capital assets.. 22,714 3,678 222,177 18,981 407,374 674,924
11 Total support (Add lines 7 through 10).           583,443,632
12
12
 
13
Section C. Computation of Public Support Percentage
14
14
94.819 %
15
15
96.050 %
16a
b
17a
b
18
Schedule A (Form 990 or 990-EZ) 2011
Schedule A (Form 990 or 990-EZ) 2011
Page 3
Part III
Support Schedule for Organizations Described in IRC 509(a)(2)
(Complete only if you checked the box on line 9 of Part I or if the organization failed to qualify under Part II. If the organization fails to qualify under the tests listed below, please complete Part II.)
Section A. Public Support
Calendar year(or fiscal year beginning in) (a) 2007 (b) 2008 (c) 2009 (d) 2010 (e) 2011 (f) Total
1 Gifts, grants, contributions, and membership fees received. (Do not include any "unusual grants.") .            
2 Gross receipts from admissions, merchandise sold or services performed, or facilities furnished in any activity that is related to the organization's tax-exempt purpose......            
3 Gross receipts from activities that are not an unrelated trade or business under section 513..            
4 Tax revenues levied for the organization's benefit and either paid to or expended on its behalf...            
5 The value of services or facilities furnished by a governmental unit to the organization without charge..            
6 Total. Add lines 1 through 5.            
7a Amounts included on lines 1, 2, and 3 received from disqualified persons...            
b Amounts included on lines 2 and 3 received from other than disqualified persons that exceed the greater of $5,000 or 1% of the amount on line 13 for the year.            
c Add lines 7a and 7b..            
8 Public Support (Subtract line 7c from line 6.)            
Section B. Total Support
Calendar year (or fiscal year beginning in) (a) 2007 (b) 2008 (c) 2009 (d) 2010 (e) 2011 (f) Total
9 Amounts from line 6...            
10a Gross income from interest, dividends, payments received on securities loans, rents, royalties and income from similar sources..            
b Unrelated business taxable income (less section 511 taxes) from businesses acquired after June 30, 1975.            
c Add lines 10a and 10b.            
11 Net income from unrelated business activities not included in line 10b, whether or not the business is regularly carried on.            
12 Other income. Do not include gain or loss from the sale of capital assets (Explain in Part IV.)            
13 Total support (Add lines 9, 10c, 11 and 12.).            
14
Section C. Computation of Public Support Percentage
15
15
 
16
16
 
Section D. Computation of Investment Income Percentage
17
17
 
18
18
 
19a
b
20
Schedule A (Form 990 or 990-EZ) 2011
Schedule A (Form 990 or 990-EZ) 2011
Page 4
Part IV
Supplemental Information. Supplemental Information. Complete this part to provide the explanation required by Part II, line 10; Part II, line 17a or 17b; or Part III, line 12. Also complete this part for any additional information. (See instructions).
Facts And Circumstances Test
 
Explanation
DESCRIPTION: GLASS ART TOUR 2007: 0 2008: 0 2009: 210,825 2010: 0 2011: 0 DESCRIPTION: OIL ROYALTIES 2007: 22,714 2008: 3,678 2009: 7,692 2010: 16,701 2011: 6,794 DESCRIPTION: NOTE RECEIVABLE INTEREST 2007: 0 2008: 0 2009: 3,660 2010: 2,280 2011: 0 DESCRIPTION: ENERGY REBATE 2007: 0 2008: 0 2009: 0 2010: 0 2011: 400,580
 
 
 
Schedule A (Form 990 or 990-EZ) 2011

Additional Data


Software ID:  
Software Version:  
Schedule B
(Form 990, 990-EZ,
or 990-PF)
Department of the Treasury
Internal Revenue Service
Schedule of Contributors
Arrow Bullet Attach to Form 990, 990-EZ, or 990-PF.
OMB No. 1545-0047
2011
Name of organization
The Salk Institute for Biological Studies
 
Employer identification number

95-2160097
Organization type (check one):
Filers of:
Section:
Form 990 or 990-EZ





Form 990-PF




Check if your organization is covered by the General Rule or a Special Rule.  
Note. Only a section 501(c)(7), (8), or (10) organization can check boxes for both the General Rule and a Special Rule. See instructions.
General Rule
Special Rules
......................... Arrow Bullet   $    
Caution. An Organization that is not covered by the General Rule and/or the Special Rules does not file Schedule B (Form 990,
990-EZ, or 990-PF), but it must answer “No” on Part IV, line 2, of its Form 990; or check the box on line H of its
Form 990-EZ or on Part I, line 2, of its Form 990-PF, to certify that it does not meet the filing requirements of Schedule B (Form 990,
990-EZ, or 990-PF).
For Paperwork Reduction Act Notice, see the Instructions
for Form 990, 990-EZ, or 990-PF.
Cat. No. 30613XSchedule B (Form 990, 990-EZ, or 990-PF) (2011)

Page 2
Schedule B (Form 990, 990-EZ, or 990-PF) (2011)
Name of organization
The Salk Institute for Biological Studies
  		Employer identification number

95-2160097
Part I
Contributors (see Instructions). Use duplicate copies of Part I if additional space is needed.
     
(a)
No.		 (b)
Name, address, and ZIP + 4		 (c)
Total contributions		 (d)
Type of contribution
RESTRICTED
RESTRICTED
 

     
RESTRICTED
RESTRICTED  
RESTRICTED, RESTRICTED   RESTRICTED

$RESTRICTED




(Complete Part II if there is a noncash contribution.)
(a)
No.		 (b)
Name, address, and ZIP + 4		 (c)
Total contributions		 (d)
Type of contribution
 
 
 

     
 
   

$  




(Complete Part II if there is a noncash contribution.)
(a)
No.		 (b)
Name, address, and ZIP + 4		 (c)
Total contributions		 (d)
Type of contribution
 
 
 

     
 
   

$  




(Complete Part II if there is a noncash contribution.)
(a)
No.		 (b)
Name, address, and ZIP + 4		 (c)
Total contributions		 (d)
Type of contribution
 
 
 

     
 
   

$  




(Complete Part II if there is a noncash contribution.)
(a)
No.		 (b)
Name, address, and ZIP + 4		 (c)
Total contributions		 (d)
Type of contribution
 
 
 

     
 
   

$  




(Complete Part II if there is a noncash contribution.)
(a)
No.		 (b)
Name, address, and ZIP + 4		 (c)
Total contributions		 (d)
Type of contribution
 
 
 

     
 
   

$  




(Complete Part II if there is a noncash contribution.)
Schedule B (Form 990, 990-EZ, or 990-PF) (2011)

Page 3
Schedule B (Form 990, 990-EZ, or 990-PF) (2011)
Name of organization
The Salk Institute for Biological Studies
  		Employer identification number

95-2160097
Part II
Noncash Property (see Instructions). Use duplicate copies of Part II if additional space is needed.
     
(a) No.
from
Part I		 (b)
Description of noncash property given		 (c)
FMV (or estimate)
(see instructions). 		(d)
Date received
 
$    
(a) No.
from
Part I		 (b)
Description of noncash property given		 (c)
FMV (or estimate)
(see instructions). 		(d)
Date received
 
$    
(a) No.
from
Part I		 (b)
Description of noncash property given		 (c)
FMV (or estimate)
(see instructions). 		(d)
Date received
 
$    
(a) No.
from
Part I		 (b)
Description of noncash property given		 (c)
FMV (or estimate)
(see instructions). 		(d)
Date received
 
$    
(a) No.
from
Part I		 (b)
Description of noncash property given		 (c)
FMV (or estimate)
(see instructions). 		(d)
Date received
 
$    
(a) No.
from
Part I		 (b)
Description of noncash property given		 (c)
FMV (or estimate)
(see instructions). 		(d)
Date received
 
$    
Schedule B (Form 990, 990-EZ, or 990-PF) (2011)

Page 4
Schedule B (Form 990, 990-EZ, or 990-PF) (2011)
Name of organization
The Salk Institute for Biological Studies
  		Employer identification number

95-2160097
Part III
Exclusively religious, charitable, etc., individual contributions to section 501(c)(7), (8), or (10) organizations
that total more than $1,000 for the year. Complete columns (a) through (e) and the following line entry.
For organizations completing Part III, enter the total of exclusively religious, charitable, etc.,
contributions of $1,000 or less for the year. (Enter this information once. See instructions.) Arrow Bullet $  
Use duplicate copies of Part III if additional space is needed
(a) No.
from
Part I		 (b)
Purpose of gift		 (c)
Use of gift		 (d)
Description of how gift is held
 
(e)
Transfer of gift
Transferee's name, address, and ZIP 4 Relationship of transferor to transferee
 
 
       
 
(a) No.
from
Part I		 (b)
Purpose of gift		 (c)
Use of gift		 (d)
Description of how gift is held
 
(e)
Transfer of gift
Transferee's name, address, and ZIP 4 Relationship of transferor to transferee
 
 
       
 
(a) No.
from
Part I		 (b)
Purpose of gift		 (c)
Use of gift		 (d)
Description of how gift is held
 
(e)
Transfer of gift
Transferee's name, address, and ZIP 4 Relationship of transferor to transferee
 
 
       
 
(a) No.
from
Part I		 (b)
Purpose of gift		 (c)
Use of gift		 (d)
Description of how gift is held
 
(e)
Transfer of gift
Transferee's name, address, and ZIP 4 Relationship of transferor to transferee
 
 
       
 
Schedule B (Form 990, 990-EZ, or 990-PF) (2011)

Additional Data


Software ID:  
Software Version:  
SCHEDULE C
(Form 990 or 990-EZ)

Department of the Treasury
Internal Revenue Service
Political Campaign and Lobbying Activities

For Organizations Exempt From Income Tax Under section 501(c) and section 527
SchCMd Bullet Complete if the organization is described below.
SchCMd Bullet Attach to Form 990 or Form 990-EZ. SchCMd Bullet See separate instructions.
OMB No. 1545-0047
2011
Open to Public
Inspection
If the organization answered “Yes” to Form 990, Part IV, Line 3, or Form 990-EZ, Part V, line 46 (Political Campaign Activities), then
Round Bullet Section 501(c)(3) organizations: Complete Parts I-A and B. Do not complete Part I-C.
Round Bullet Section 501(c) (other than section 501(c)(3)) organizations: Complete Parts I-A and C below. Do not complete Part I-B.
Round Bullet Section 527 organizations: Complete Part I-A only.
If the organization answered “Yes” to Form 990, Part IV, Line 4, or Form 990-EZ, Part VI, line 47 (Lobbying Activities), then
Round Bullet Section 501(c)(3) organizations that have filed Form 5768 (election under section 501(h)) Complete Part II-A. Do not complete Part II-B.
Round Bullet Section 501(c)(3) organizations that have NOT filed Form 5768 (election under section 501(h)): Complete Part II-B. Do not complete Part II-A.
If the organization answered “Yes” to Form 990, Part IV, Line 5 (Proxy Tax) or Form 990-EZ, line 35c (Proxy Tax), then
Round Bullet Section 501(c)(4), (5), or (6) organizations: Complete Part III.
Name of the organization
The Salk Institute for Biological Studies
 
Employer identification number

95-2160097
Part I-A
Complete if the organization is exempt under section 501(c) or is a section 527 organization.

1
Provide a description of the organization’s direct and indirect political campaign activities in Part IV.
2
Political expenditures ....................................SchCMd Bullet
$  
3
Volunteer hours ........................................
 

Part I-B
Complete if the organization is exempt under section 501(c)(3).
1
Enter the amount of any excise tax incurred by the organization under section 4955 .........SchCMd Bullet
$  
2
Enter the amount of any excise tax incurred by organization managers under section 4955 ......SchCMd Bullet
$  
3
If the organization incurred a section 4955 tax, did it file Form 4720 for this year? ..............
4a
Was a correction made? .........................................
b
If "Yes," describe in Part IV.
Part I-C
Complete if the organization is exempt under section 501(c) except section 501(c)(3).
1
Enter the amount directly expended by the filing organization for section 527 exempt function activities SchCMd Bullet
$  
2
Enter the amount of the filing organization's funds contributed to other organizations for section 527 exempt function activities ...................................SchCMd Bullet

$  
3
Total exempt function expenditures. Add lines 1 and 2. Enter here and on Form 1120-POL, line 17b..SchCMd Bullet

$  
4
Did the filing organization file Form 1120-POL for this year? ..........................
5
Enter the names, addresses and employer identification number (EIN) of all section 527 political organizations to which the filing
organization made payments. For each organization listed, enter the amount paid from the filing organization’s funds. Also enter the amount of political contributions received that were promptly and directly delivered to a separate political organization, such as a separate segregated fund or a political action committee (PAC). If additional space is needed, provide information in Part IV.
(a) Name (b) Address (c) EIN (d) Amount paid from filing organization's funds. If none, enter -0-. (e) Amount of political contributions received and promptly and directly delivered to a separate political organization. If none, enter -0-.










For Privacy Act and Paperwork Reduction Act Notice, see the instructions for Form 990.
Cat. No. 50084S
Schedule C (Form 990 or 990-EZ) 2011

Schedule C (Form 990 or 990-EZ) 2011
Page 2
Part II-A
Complete if the organization is exempt under section 501(c)(3) and filed Form 5768 (election under section 501(h)).
A Check expenses, and share of excess lobbying expenditures).
B Check
Limits on Lobbying Expenditures
(The term "expenditures" means amounts paid or incurred.) 		(a) Filing
organization's
totals 		(b) Affiliated group
totals
1a Total lobbying expenditures to influence public opinion (grass roots lobbying) ......    
b Total lobbying expenditures to influence a legislative body (direct lobbying) .......    
c Total lobbying expenditures (add lines 1a and 1b) ...................    
d Other exempt purpose expenditures ........................    
e Total exempt purpose expenditures (add lines 1c and 1d) ...............    
f Lobbying nontaxable amount. Enter the amount from the following table in both
columns.		    
  If the amount on line 1e, column (a) or (b) is:The lobbying nontaxable amount is:    
  Not over $500,00020% of the amount on line 1e.    
  Over $500,000 but not over $1,000,000$100,000 plus 15% of the excess over $500,000.    
  Over $1,000,000 but not over $1,500,000$175,000 plus 10% of the excess over $1,000,000.    
  Over $1,500,000 but not over $17,000,000$225,000 plus 5% of the excess over $1,500,000.    
  Over $17,000,000$1,000,000.    
       
g Grassroots nontaxable amount (enter 25% of line 1f) .................    
h Subtract line 1g from line 1a. If zero or less, enter -0-. ................    
i Subtract line 1f from line 1c. If zero or less, enter -0-. ................    
j If there is an amount other than zero on either line 1h or line 1i, did the organization file Form 4720 reporting
section 4911 tax for this year? ......................................

4-Year Averaging Period Under Section 501(h)
(Some organizations that made a section 501(h) election do not have to complete all of the five
columns below. See the instructions for lines 2a through 2f on page 4.)
Lobbying Expenditures During 4-Year Averaging Period
  Calendar year (or fiscal year
beginning in) 		(a) 2008 (b) 2009 (c) 2010 (d) 2011 (e) Total
             
2a Lobbying non-taxable amount          
             
b Lobbying ceiling amount
(150% of line 2a, column(e)) 		         
             
c Total lobbying expenditures          
             
d Grassroots nontaxable amount          
             
e Grassroots ceiling amount
(150% of line 2d, column (e))		          
             
f Grassroots lobbying expenditures          
Schedule C (Form 990 or 990-EZ) 2011


Schedule C (Form 990 or 990-EZ) 2011
Page 3
Part II-B
Complete if the organization is exempt under section 501(c)(3) and has NOT filed Form 5768 (election under section 501(h)).
For each “Yes” response to lines 1a through 1i below, provide in Part IV a detailed description of the lobbying activity.
(a)
Yes
No
(b)
Amount
1
During the year, did the filing organization attempt to influence foreign, national, state or local legislation, including any attempt to influence public opinion on a legislative matter or referendum, through the use of:
a
Volunteers? .........................................
 
No
b
Paid staff or management (include compensation in expenses reported on lines 1c through 1i)? ....
 
No
c
Media advertisements? ....................................
 
No
 
d
Mailings to members, legislators, or the public? .........................
 
No
 
e
Publications, or published or broadcast statements? .......................
 
No
 
f
Grants to other organizations for lobbying purposes? .......................
 
No
 
g
Direct contact with legislators, their staffs, government officials, or a legislative body? ........
 
No
 
h
Rallies, demonstrations, seminars, conventions, speeches, lectures, or any similar means? ......
 
No
 
i
Other activities? ..........................
Yes
 
2,930
j
Total. Add lines 1c through 1i ...............................
2,930
2a
Did the activities in line 1 cause the organization to be not described in section 501(c)(3)? .....
 
No
b
If "Yes," enter the amount of any tax incurred under section 4912 .................
 
c
If "Yes," enter the amount of any tax incurred by organization managers under section 4912 .....
 
d
If the filing organization incurred a section 4912 tax, did it file Form 4720 for this year? .......
 
 
Part III-A
Complete if the organization is exempt under section 501(c)(4), section 501(c)(5), or section 501(c)(6).
Yes
No
1
Were substantially all (90% or more) dues received nondeductible by members? ................
1
 
 
2
Did the organization make only in-house lobbying expenditures of $2,000 or less? ................
2
 
 
3
Did the organization agree to carry over lobbying and political expenditures from the prior year? ..........
3
 
 
Part III-B
Complete if the organization is exempt under section 501(c)(4), section 501(c)(5), or section 501(c)(6) and if either (a) BOTH Part III-A, lines 1 and 2 are answered “No” OR (b) Part III-A, line 3 is answered “Yes”.
1
Dues, assessments and similar amounts from members .....................
1
 
2
Section 162(e) nondeductible lobbying and political expenditures (do not include amounts of political
expenses for which the section 527(f) tax was paid).
a
Current year .........................................
2a
 
b
Carryover from last year ....................................
2b
 
c
Total ...........................................
2c
 
3
Aggregate amount reported in section 6033(e)(1)(A) notices of nondeductible section 162(e) dues .
3
 
4
If notices were sent and the amount on line 2c exceeds the amount on line 3, what portion of the excess does the organization agree to carryover to the reasonable estimate of nondeductible lobbying and political expenditure next year? ................................
4
 
5
Taxable amount of lobbying and political expenditures (see instructions) ..............
5
 
Part IV
Supplemental Information
Complete this part to provide the descriptions required for Part l-A, line 1; Part l-B, line 4; Part l-C, Part II-A; line 5; and Part ll-B, line 1.
Also, complete this part for any additional information.
Identifier Return Reference Explanation
OTHER ACTIVITIES PART II-B, LINE 1i PAID MEMBERSHIP DUES TO RESEARCH AND BIOMEDICAL ORGANIZATIONS, A PORTION OF WHICH ARE CONSIDERED LOBBYING. ASSOCIATION OF INDEPENDENT RESEARCH INSTITUTES $ 720 CALIFORNIA HEALTHCARE INSTITUTE $1,250 NATIONAL ASSOCIATION FOR BIOMEDICAL RESEARCH $ 960
Schedule C (Form 990 or 990EZ) 2011

Additional Data


Software ID:  
Software Version:  

SCHEDULE D
(Form 990)
Department of the Treasury
Internal Revenue Service
Supplemental Financial Statements
SchDMd Bullet Complete if the organization answered "Yes," to Form 990,
Part IV, line 6, 7, 8, 9, 10, 11a, 11b, 11c, 11d, 11e, 11f, 12a, or 12b
SchDMd Bullet Attach to Form 990. SchDMd Bullet See separate instructions.
OMB No. 1545-0047
2011
Open to Public Inspection
Name of the organization
The Salk Institute for Biological Studies
 
Employer identification number

95-2160097
Part I
Organizations Maintaining Donor Advised Funds or Other Similar Funds or Accounts. Complete if the organization answered "Yes" to Form 990, Part IV, line 6.
(a) Donor advised funds (b) Funds and other accounts
1 Total number at end of year .......    
2 Aggregate contributions to (during year) ...    
3 Aggregate grants from (during year) ...    
4 Aggregate value at end of year .......    
5
Did the organization inform all donors and donor advisors in writing that the assets held in donor advised
funds are the organization's property, subject to the organization's exclusive legal control? ............
6
Did the organization inform all grantees, donors, and donor advisors in writing that grant funds can be
used only for charitable purposes and not for the benefit of the donor or donor advisor, or for any other purpose conferring impermissible private benefit? ...................................
Part II
Conservation Easements. Complete if the organization answered "Yes" to Form 990, Part IV, line 7.
1
Purpose(s) of conservation easements held by the organization (check all that apply).
2
Complete lines 2a through 2d if the organization held a qualified conservation contribution in the form of a conservation easement on the last day of the tax year.
Held at the End of the Year
a Total number of conservation easements ....................... 2a  
b Total acreage restricted by conservation easements .................. 2b  
c Number of conservation easements on a certified historic structure included in (a) ..... 2c  
d Number of conservation easements included in (c) acquired after 8/17/06, and not on a historic structure listed in the National Register .................... 2d  
3
Number of conservation easements modified, transferred, released, extinguished, or terminated by the organization during
the tax year SchDMd Bullet  
4
Number of states where property subject to conservation easement is located SchDMd Bullet  
5
Does the organization have a written policy regarding the periodic monitoring, inspection, handling of violations, and
enforcement of the conservation easements it holds? .............................
6
Staff and volunteer hours devoted to monitoring, inspecting and enforcing conservation easements during the year SchDMd Bullet  
7
Amount of expenses incurred in monitoring, inspecting, and enforcing conservation easements during the year
SchDMd Bullet $  
8
Does each conservation easement reported on line 2(d) above satisfy the requirements of section
170(h)(4)(B)(i) and 170(h)(4)(B)(ii)? ....................................
9
In Part XIV, describe how the organization reports conservation easements in its revenue and expense statement, and
balance sheet, and include, if applicable, the text of the footnote to the organization’s financial statements that describes
the organization’s accounting for conservation easements.
Part III
Organizations Maintaining Collections of Art, Historical Treasures, or Other Similar Assets.
Complete if the organization answered "Yes" to Form 990, Part IV, line 8.
1a
If the organization elected, as permitted under SFAS 116 (ASC 958), not to report in its revenue statement and balance sheet works of
art, historical treasures, or other similar assets held for public exhibition, education or research in furtherance of public service,
provide, in Part XIV, the text of the footnote to its financial statements that describes these items.
b
If the organization elected, as permitted under SFAS 116 (ASC 958), to report in its revenue statement and balance sheet works of art,
historical treasures, or other similar assets held for public exhibition, education, or research in furtherance of public service,
provide the following amounts relating to these items:
(i)
Revenues included in Form 990, Part VIII, line 1 ........................SchDMd Bullet $  
(ii)
Assets included in Form 990, Part X ..............................SchDMd Bullet $  
2
If the organization received or held works of art, historical treasures, or other similar assets for financial gain, provide the
following amounts required to be reported under SFAS 116 (ASC 958), relating to these items:
a
Revenues included in Form 990, Part VIII, line 1 ..........................SchDMd Bullet $  
b
Assets included in Form 990, Part X ...............................SchDMd Bullet $  
For Privacy Act and Paperwork Reduction Act Notice, see the Intructions for Form 990
Cat. No. 52283D
Schedule D (Form 990) 2011

Schedule D (Form 990) 2011
Page 2
Part III
Organizations Maintaining Collections of Art, Historical Treasures, or Other Similar Assets (continued)
3
Using the organization’s accession and other records, check any of the following that are a significant use of its collection
items (check all that apply):
a
d
b
e
 
c
4
Provide a description of the organization’s collections and explain how they further the organization’s exempt purpose in
Part XIV.
5
During the year, did the organization solicit or receive donations of art, historical treasures or other similar
assets to be sold to raise funds rather than to be maintained as part of the organization’s collection?........
Part IV
Escrow and Custodial Arrangements. Complete if the organization answered "Yes" to Form 990,
Part IV, line 9, or reported an amount on Form 990, Part X, line 21.
1a
Is the organization an agent, trustee, custodian or other intermediary for contributions or other assets not
included on Form 990, Part X? ....................................
b
If "Yes," explain the arrangement in Part XIV and complete the following table:
Amount
c Beginning balance ................................. 1c  
d Additions during the year .............................. 1d  
e Distributions during the year ............................. 1e  
f Ending balance ................................... 1f  
2a
Did the organization include an amount on Form 990, Part X, line 21? .....................
b
If “Yes,” explain the arrangement in Part XIV.
Part V
Endowment Funds. Complete if the organization answered "Yes" to Form 990, Part IV, line 10.
(a)Current Year (b)Prior Year (c)Two Years Back (d)Three Years Back (e)Four Years Back
1a Beginning of year balance .... 113,493,623 89,420,545 71,360,759 83,049,682
b Contributions ........ 18,776,974 12,288,420 11,356,891 2,721,386
c Net investment earnings, gains, and losses ... -1,376,528 15,274,598 8,833,640 -12,462,264
d Grants or scholarships .....        
e Other expenditures for facilities
and programs ........ 		4,168,510 3,489,940 2,130,745 1,948,045
f Administrative expenses ....        
g End of year balance ...... 126,725,559 113,493,623 89,420,545 71,360,759
2
Provide the estimated percentage of the year end balance (line 1g) held as:
a
Board designated or quasi-endowment SchDMd Bullet0.710 %
b
Permanent endowment SchDMd Bullet99.290 %
c
Temporarily restricted endowment SchDMd Bullet  
The percentages in lines 2a, 2b, and 2c should equal 100%.
3a
Are there endowment funds not in the possession of the organization that are held and administered for the
organization by:

Yes
No
(i) unrelated organizations ........................
3a(i)
 
No
(ii) related organizations ........................
3a(ii)
 
No
b
If "Yes" to 3a(ii), are the related organizations listed as required on Schedule R? .........
3b
 
 
4
Describe in Part XIV the intended uses of the organization's endowment funds.
Part VI
Land, Buildings, and Equipment. See Form 990, Part X, line 10.
Description of property (a) Cost or other basis (investment) (b)Cost or other basis (other) (c) Accumulated depreciation (d) Book value
1a Land .................   1,153,930 1,153,930
b Buildings ................   68,485,570 37,427,293 31,058,277
c Leasehold improvements ............   70,556,093 38,884,018 31,672,075
d Equipment ................   70,199,675 49,753,879 20,445,796
e Other .................   3,475,378   3,475,378
Total. Add lines 1a through 1e. (Column (d) must equal Form 990, Part X, column (B), line 10(c).).......SchDMdBullet 87,805,456
Schedule D (Form 990) 2011

Schedule D (Form 990) 2011
Page 3
Part VII
Investments—Other Securities. See Form 990, Part X, line 12.
(a) Description of security or category
(including name of security)		 (b)Book value (c) Method of valuation:
Cost or end-of-year market value
(1)Financial derivatives    
(2)Closely-held equity interests    
(3)Other
(A) ALTERNATIVE INVESTMENTS 		100,030,879 F

(B) STOCKS NOT-PUBLICLY TRADED <5% 		3,114 C







Total. (Column (b) must equal Form 990, Part X, col. (B) line 12.)Small Bullet 100,033,993
Part VIII
Investments—Program Related. See Form 990, Part X, line 13.
(a) Description of investment type (b) Book value (c) Method of valuation:
Cost or end-of-year market value








Total. (Column (b) must equal Form 990, Part X, col.(B) line 13.)Small Bullet  
Part IX
Other Assets. See Form 990, Part X, line 15.
(a) Description (b) Book value








Total. (Column (b) must equal Form 990, Part X, col.(B) line 15.)...........Small Bullet  
Part X
Other Liabilities. See Form 990, Part X, line 25.
1.(a) Description of Liability (b) Book value
Federal Income Taxes 2,052
DEFERRED RETIREMENT OBLIGATION 6,889,424








Total. (Column (b) must equal Form 990, Part X, col.(B) line 25.)Small Bullet 6,891,476
2. Fin 48 (ASC 740) Footnote. In Part XIV, provide the text of the footnote to the organization's financial statements that reports the organization's liability for uncertain tax positions under FIN 48 (ASC740).
Schedule D (Form 990) 2011

Schedule D (Form 990) 2011
Page 4
Part XI Reconciliation of Change in Net Assets from Form 990 to Financial Statements
1 Total revenue (Form 990, Part VIII, column (A), line 12) .................... 1 149,205,521
2 Total expenses (Form 990, Part IX, column (A), line 25) ..................... 2 120,052,020
3 Excess or (deficit) for the year. Subtract line 2 from line 1 ............. 3 29,153,501
4 Net unrealized gains (losses) on investments .......................... 4 -8,223,913
5 Donated services and use of facilities ............................. 5  
6 Investment expenses ................................... 6  
7 Prior period adjustments .................................. 7  
8 Other (Describe in Part XIV.) ................................. 8 11,554,613
9 Total adjustments (net). Add lines 4 through 8 ......................... 9 3,330,700
10 Excess or (deficit) for the year per financial statements. Combine lines 3 and 9 ......... 10 32,484,201
Part XII Reconciliation of Revenue per Audited Financial Statements With Revenue per Return
1 Total revenue, gains, and other support per audited financial statements ....... 1 152,756,405
2 Amounts included on line 1 but not on Form 990, Part VIII, line 12:
a Net unrealized gains on investments .......... 2a -8,223,913
b Donated services and use of facilities ......... 2b  
c Recoveries of prior year grants ........... 2c  
d Other (Describe in Part XIV.) ............ 2d 11,553,614
e Add lines 2a through 2d ..................... 2e 3,329,701
3 Subtract line 2e from line 1..................... 3 149,426,704
4 Amounts included on Form 990, Part VIII, line 12, but not on line 1:
a Investment expenses not included on Form 990, Part VIII, line 7b . 4a  
b Other (Describe in Part XIV.) ........... 4b -221,183
c Add lines 4a and 4b....................... 4c -221,183
5 Total Revenue. Add lines 3 and 4c. (This must equal Form 990, Part I, line 12.) ...... 5 149,205,521
Part XIII Reconciliation of Expenses per Audited Financial Statements With Expenses per Return
1 Total expenses and losses per audited financial statements ............. 1 120,273,202
2 Amounts included on line 1 but not on Form 990, Part IX, line 25:
a Donated services and use of facilities .......... 2a  
b Prior year adjustments .............. 2b  
c Other losses ................ 2c  
d Other (Describe in Part XIV.) ............ 2d 221,183
e Add lines 2a through 2d...................... 2e 221,183
3 Subtract line 2e from line 1..................... 3 120,052,019
4 Amounts included on Form 990, Part IX, line 25, but not on line 1:
a Investment expenses not included on Form 990, Part VIII, line 7b .. 4a  
b Other (Describe in Part XIV.) ............ 4b 1
c Add lines 4a and 4b....................... 4c 1
5 Total expenses. Add lines 3 and 4c. (This must equal Form 990, Part I, line 18.) ...... 5 120,052,020
Part XIV
Supplemental Information
Complete this part to provide the descriptions required for Part II, lines 3, 5, and 9; Part III, lines 1a and 4; Part lV, lines 1b and 2b;
Part V, line 4; Part X; Part XI, line 8; Part XII, lines 2d and 4b; and Part XIII, lines 2d and 4b. Also complete this part to provide any additional information.
Identifier Return Reference Explanation
CHANGE IN NET ASSETS Part XI, Line 8 Other Investment gains in excess of amount designated for current operations under spending policy plus rounding.
RECONCILIATION OF REVENUE PER AUDITED FS WITH REVENUE PER RETURN Part XII, Lines 2d Investment return in excess of amount designated for current operations under spending policy plus rounding.
Reconciliation of Revenue per Audited FS with Revenue per Return Part XII, Line 4b Fundraising events expenses.
ENDOWMENT FUNDS USES PART V, LINE 4 ENDOWMENT INCOME INTENDED TO BE USED FOR AND TO SUPPORT RESEARCH, OPERATIONS, AND LECTURESHIP EXPENSES.
Reconciliation of Expenses per Audited FS with Expenses per Return Part XIII, Line 2d Fundraising events expenses.
Reconciliation of Expenses per Audited Financial Stmts w Expenses per Rtn Part XIII, Line 4b Rounding.
Schedule D (Form 990) 2011

Additional Data


Software ID:  
Software Version:  




SCHEDULE F(Form 990)
Department of the Treasury
Internal Revenue Service
Statement of Activities Outside the United States
Right pointing arrow large image Complete if the organization answered "Yes" to Form 990,Part IV, line 14b, 15, or 16.Right pointing arrow large image Attach to Form 990. Right pointing arrow large image See separate instructions.
OMB No. 1545-0047
2011
Open to Public Inspection
Name of the organization
The Salk Institute for Biological Studies
 
Employer identification number

95-2160097
Part I
General Information on Activities Outside the United States. Complete if the organization answered
“Yes” to Form 990, Part IV, line 14b.
1
For grantmakers. Does the organization maintain records to substantiate the amount of its grants
and other assistance, the grantees' eligibility for the grants or assistance, and the selection criteria used
to award the grants or assistance? ..............................
2
For grantmakers. Describe in Part V the organization’s procedures for monitoring the use of its grants and other
assistance outside the United States.
3
Activites per Region. (Use Part V if additional space is needed.)
(a) Region (b) Number of offices in the region (c) Number of employees or agents in region or independent contractors (d) Activities conducted in region (by type) (e.g., fundraising, program services, investments, grants to recipients located in the region) (e) If activity listed in (d) is a program service, describe specific type of
service(s) in region		 (f) Total
expenditures for region/investments
in region
Europe (Including Iceland and Greenland)     Program Services Attended conference 140,475
East Asia and the Pacific     Program Services Attended conference 53,892
Central America and the Caribbean     Program Services Attended conference 8,510
Middle East and North Africa     Program Services Attended conference 6,061
North America     Program Services Attended conference 20,661
South Asia     Program Services Attended conference 1,889
South America     Program Services Attended conference 862
North America     Program Services Scientific subcontract 138,631
Europe (Including Iceland and Greenland)     Program Services Scientific subcontract 74,435
South America     Program Services Scientific subcontract 48,339
East Asia and the Pacific     Program Services Scientifc subcontract 9,700
Central America and the Caribbean     Investments   72,857,682
           
           
           
           
           
3a Sub-total .....     73,361,137
b Total from continuation sheets to Part I ...      
c Totals (add lines 3a and 3b)     73,361,137
For Privacy Act and Paperwork Reduction Act Notice, see the Instructions for Form 990.Cat. No. 50082W Schedule F (Form 990) 2011
Schedule F (Form 990) 2011
Page 2
Part II
Grants and Other Assistance to Organizations or Entities Outside the United States. Complete if the organization answered "Yes" to Form 990,
Part IV, line 15, for any recipient who received more than $5,000. Check this box if no one recipient received more than $5,000 ........ MediumBullet
Use Part V if additional space is needed.
1 (a) Name of organization (b) IRS code section
and EIN (if applicable)		 (c) Region (d) Purpose of
grant 		(e) Amount of
cash grant 		(f) Manner of
cash
disbursement 		(g) Amount of
of non-cash
assistance 		(h) Description
of non-cash
assistance 		(i) Method of
valuation
(book, FMV,
appraisal, other)
             
             
             
             
             
             
             
             
             
             
             
             
             
             
             
             
2
Enter total number of recipient organizations listed above that are recognized as charities by the foreign country, recognized as tax-exempt by the IRS, or for which the grantee or counsel has provided a section 501(c)(3) equivalency letter .....MediumBullet
 
3
Enter total number of other organizations or entities ........................MediumBullet
 
Schedule F (Form 990) 2011
Schedule F (Form 990) 2011Page 3
Part III
Grants and Other Assistance to Individuals Outside the United States. Complete if the organization answered "Yes" to Form 990, Part IV, line 16.
Use Part V if additional space is needed.
(a) Type of grant or assistance (b) Region (c) Number of recipients (d) Amount of
cash grant 		(e) Manner of cash
disbursement 		(f) Amount of
non-cash
assistance 		(g) Description
of non-cash
assistance 		(h) Method of
valuation
(book, FMV,
appraisal, other)
               
               
               
               
               
               
               
               
               
               
               
               
               
               
               
               
               
               
Schedule F (Form 990) 2011
Schedule F (Form 990) 2011
Page 4
Part IV
Foreign Forms
1 Was the organization a U.S. transferor of property to a foreign corporation during the tax year? If "Yes," the organization may be required to file Form 926 (see instructions for Form 926).................
2 Did the organization have an interest in a foreign trust during the tax year? If " Yes," the organization may be required to file Form 3520 and/or Form 3520-A. (see instructions for Forms 3520 and 3520-A)..........
3 Did the organization have an ownership interest in a foreign corporation during the tax year? If "Yes," the organization may be required to file Form 5471, Information Return of U.S. Persons with respect to Certain Foreign Corporations. (see instructions for Form 5471)..............................
4 Was the organization a direct or indirect shareholder of a passive foreign investment company or a qualified electing fund during the tax year? If "Yes," the organization may be required to file Form 8621, Return by a Shareholder of a Passive Foreign Investment Company or Qualified Electing Fund. (see instructions for Form 8621)
5 Did the organization have an ownership interest in a foreign partnership during the tax year? If "Yes," the organization may be required to file Form 8865, Return of U.S. Persons with respect to Certain Foreign Partnerships. (see instructions for Form 8865)....................................
6 Did the organization have any operations in or related to any boycotting countries during the tax year? If "Yes," the organization may be required to file Form 5713, International Boycott Report (see instructions for Form 5713)................................................
Schedule F (Form 990) 2011
Schedule F (Form 990) 2011
Page 5
Part V
Supplemental Information
Complete this part to provide the information required by Part I, line 2 (monitoring of funds); Part I, line 3, column (f) (accounting method; amounts of investments vs. expenditures per region); Part II, line 1 (accounting method); Part III (accounting method); and Part III, column (c) (estimated number of recipients), as applicable. Also complete this part to provide any additional information (see instructions).
Identifier ReturnReference Explanation
NO. OF EMPLOYEES IN THE REGION PART I, LINE 3, COLUMN (C) SCIENTISTS TRAVEL TO FOREIGN COUNTRIES TO ATTEND CONFERENCES. WE DO NOT DEEM THESE ACTIVITIES TO CONSTITUTE WORKING IN THE REGION.
ACCOUNTING METHOD PART I, LINE 3, COLUMN (F) ACCRUAL METHOD
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
Schedule F (Form 990) 2011
Additional Data


Software ID:  
Software Version:  



SCHEDULE G (Form 990 or 990-EZ)
Department of the Treasury
Internal Revenue Service
Supplemental Information Regarding
Fundraising or Gaming Activities
Complete if the organization answered "Yes" to Form 990, Part IV, lines 17, 18, or 19,or if the organization entered more than $15,000 on Form 990-EZ, line 6a.right arrowAttach to Form 990 or Form 990-EZ. right arrowSee separate instructions.
OMB No. 1545-0047
2011
Open to Public Inspection
Name of the organization
The Salk Institute for Biological Studies
 
Employer identification number

95-2160097
Part I
Fundraising Activities. Complete if the organization answered "Yes" to Form 990, Part IV, line 17.
1
Indicate whether the organization raised funds through any of the following activities. Check all that apply.
a e
b f
c g
d
2a
Did the organization have a written or oral agreement with any individual (including officers, directors, trustees
or key employees listed in Form 990, Part VII) or entity in connection with professional fundraising services?
b
If “Yes,” list the ten highest paid individuals or entities (fundraisers) pursuant to agreements under which the fundraiser is
to be compensated at least $5,000 by the organization. Form 990-EZ filers are not required to complete this table.
(i) Name and address of individual
or entity (fundraiser) 		(ii) Activity (iii) Did fundraiser have custody or control of contributions? (iv) Gross receipts
from activity 		(v) Amount paid to
(or retained by)
fundraiser listed in
col. (i) 		(vi) Amount paid to
(or retained by)
organization
Yes No
Total .................right arrow      
3
List all states in which the organization is registered or licensed to solicit funds or has been notified it is exempt from registration or licensing.
For Privacy Act and Paperwork Reduction Act Notice, see the Instructions for Form 990.
Cat. No. 50083H
Schedule G (Form 990 or 990-EZ) 2011
Schedule G (Form 990 or 990-EZ) 2011
Page 2
Part II
Fundraising Events. Complete if the organization answered "Yes" to Form 990, Part IV, line 18, or reported more than $15,000 on Form 990-EZ, line 6a. List events with gross receipts greater than $5,000.
(a) Event #1

CONCERT
(event type) 		(b) Event #2

GOLF TOURNAMENT
(event type) 		(c) Other Events

0
(total number) 		(d) Total Events
(Add col. (a) through col. (c))
VerticalRevenue 1 Gross receipts . . . 690,282 34,500 0 724,782
2 Less: Charitable
contributions . . . 		555,957 24,900 0 580,857
3 Gross income (line 1
minus line 2) . . . 		134,325 9,600 0 143,925
VerticalDirectExpenses 4 Cash prizes . . .        
5 Non-cash prizes . .        
6 Rent/facility costs . .        
7 Food and beverages . . 84,600 11,583 0 96,183
8 Entertainment . . . 125,000   0 125,000
9 Other direct expenses .        
10 Direct expense summary. Add lines 4 through 9 in column (d) ........... right arrow 221,183
11 Net income summary. Combine lines 3 and 10 in column (d)............ right arrow -77,258
Part III
Gaming. Complete if the organization answered "Yes" to Form 990, Part IV, line 19, or reported more than $15,000 on Form 990-EZ, line 6a.
VerticalRevenue (a) Bingo (b) Pull tabs/Instant
bingo/progressive bingo 		(c) Other gaming (d) Total gaming (Add col. (a) through col. (c))
1 Gross revenue . . . .        
VerticalDirectExpenses 2 Cash prizes . . . .        
3 Non-cash prizes . . .        
4 Rent/facility costs . . .        
5 Other direct expenses . .        
6 Volunteer labor . . .
 
 
 
7 Direct expense summary. Add lines 2 through 5 in column (d) ........... right arrow  
8 Net gaming income summary. Combine lines 1 and 7 in column (d) .......... right arrow  
9
Enter the state(s) in which the organization operates gaming activities:
a
Is the organization licensed to operate gaming activities in each of these states? ............
b
If "No," Explain:
 
10a
Were any of the organization's gaming licenses revoked, suspended or terminated during the tax year? .....
b
If "Yes," Explain:
 
11
Does the organization operate gaming activities with nonmembers? .................
12
Is the organization a grantor, beneficiary or trustee of a trust or a member of a partnership or other entity
formed to administer charitable gaming? ..........................
Schedule G (Form 990 or 990-EZ) 2011
Schedule G (Form 990 or 990-EZ) 2011
Page 3
13
Indicate the percentage of gaming activity operated in:
a
The organization's facility ......................
13a
 
b
An outside facility ........................
13b
 
14
Provide the name and address of the person who prepares the organization's gaming/special events books and records:
Name right arrow
Address right arrow
15a
Does the organization have a contract with a third party from whom the organization receives gaming
revenue? ......................................
b
If "Yes," enter the amount of gaming revenue received by the organization right arrow $   and the
amount of gaming revenue retained by the third party right arrow $   .
c
If "Yes," enter name and address:
Name right arrow
Address right arrow
 
 
16
Gaming manager information:
Name right arrow
Gaming manager compensation right arrow $  
Description of services provided right arrow
 
17
Mandatory distributions:
a
Is the organization required under state law to make charitable distributions from the gaming proceeds to
retain the state gaming license? ............................
b
Enter the amount of distributions required under state law distributed to other exempt organizations or spent
in the organization's own exempt activities during the tax year right arrow$  
Part IV
Complete this part to provide additional information for responses to quuestion on Schedule G (see instructions.)
Identifier ReturnReference Explanation
Schedule G (Form 990 or 990-EZ) 2011
Additional Data


Software ID:  
Software Version:  
Schedule J
(Form 990)
Department of the Treasury
Internal Revenue Service
Compensation Information
For certain Officers, Directors, Trustees, Key Employees, and Highest
Compensated Employees
SchJMediumBullet Complete if the organization answered "Yes" to Form 990,
Part IV, question 23.
SchJMediumBullet Attach to Form 990. SchJMediumBullet See separate instructions.
OMB No. 1545-0047
2011
Open to Public Inspection
Name of the organization
The Salk Institute for Biological Studies
 
Employer identification number

95-2160097
Part I
Questions Regarding Compensation
Yes
No
1a
Check the appropiate box(es) if the organization provided any of the following to or for a person listed in Form
990, Part VII, Section A, line 1a. Complete Part III to provide any relevant information regarding these items.
b
If any of the boxes in line 1a are checked, did the organization follow a written policy regarding payment or reimbursement or provision of all the expenses described above? If "No," complete Part III to explain....
1b
Yes
 
2
Did the organization require substantiation prior to reimbursing or allowing expenses incurred by all
officers, directors, trustees, and the CEO/Executive Director, regarding the items checked in line 1a? ....
2
Yes
 
3
Indicate which, if any, of the following the organization uses to establish the compensation of the
organization's CEO/Executive Director. Check all that apply. Do not check any boxes for methods
used by a related organization to establish compensation of the CEO/Executive Director, but explain in Part III.
4
During the year, did any person listed in Form 990, Part VII, Section A, line 1a with respect to the filing organization or a related organization:
a
Receive a severance payment or change-of-control payment? ...............
4a
 
No
b
Participate in, or receive payment from, a supplemental nonqualified retirement plan? ........
4b
Yes
 
c
Participate in, or receive payment from, an equity-based compensation arrangement? ........
4c
 
No
If "Yes" to any of lines 4a-c, list the persons and provide the applicable amounts for each item in Part III.
Only 501(c)(3) and 501(c)(4) organizations only must complete lines 5-9.
5
For persons listed in form 990, Part VII, Section A, line 1a, did the organization pay or accrue any
compensation contingent on the revenues of:
a
The organization? ...........................
5a
 
No
b
Any related organization? .........................
5b
 
No
If "Yes," to line 5a or 5b, describe in Part III.
6
For persons listed in form 990, Part VII, Section A, line 1a, did the organization pay or accrue any
compensation contingent on the net earnings of:
a
The organization? ...........................
6a
 
No
b
Any related organization? .........................
6b
 
No
If "Yes," to line 6a or 6b, describe in Part III.
7
For persons listed in Form 990, Part VII, Section A, line 1a, did the organization provide any non-fixed
payments not described in lines 5 and 6? If "Yes," describe in Part III ............
7
Yes
 
8
Were any amounts reported in Form 990, Part VII, paid or accured pursuant to a contract that was
subject to the initial contract exception described in Regulations section 53.4958-4(a)(3)? If "Yes," describe
in Part III .............................
8
 
No
9
If "Yes" to line 8, did the organization also follow the rebuttable presumption procedure described in Regulations section 53.4958-6(c)? .........................
9
 
 
For Privacy Act and Paperwork Reduction Act Notice, see the Intructions for Form 990
Cat. No. 50053T
Schedule J (Form 990) 2011

Schedule J (Form 990) 2011
Page 2
Part II
Officers, Directors, Trustees, Key Employees, and Highest Compensated Employees. Use duplicate copies if additional space is needed.
For each individual whose compensation must be reported in Schedule J, report compensation from the organization on row (i) and from related organizations, described in the
instructions on row (ii). Do not list any individuals that are not listed on Form 990, Part VII.

Note. The sum of columns (B)(i)-(iii) for each listed individual must equal the total amount of Form 990, Part VII, Section A, line 1a, applicable column (D) and column (E) for that individual.
(A) Name (B) Breakdown of W-2 and/or 1099-MISC compensation (C) Retirement and other deferred compensation (D) Nontaxable
benefits		 (E) Total of columns
(B)(i)-(D) 		(F) Compensation
reported as deferred
in prior Form 990
(i) Base compensation (ii) Bonus & incentive compensation (iii) Other reportable compensation
(1) William R Brody MD PhD (i)
(ii)		 642,174
0 		0
0 		160,668
0 		131,850
0 		12,131
0 		946,823
0 		0
0
(2) Thomas D Albright PhD (i)
(ii)		 231,616
0 		0
0 		2,214
0 		31,096
0 		15,664
0 		280,590
0 		0
0
(3) Christoper R Kintner PHD (i)
(ii)		 185,376
0 		0
0 		17,738
0 		26,000
0 		5,266
0 		234,380
0 		0
0
(4) Geoffrey M Wahl PhD (i)
(ii)		 243,831
0 		0
0 		3,580
0 		31,850
0 		15,377
0 		294,638
0 		0
0
(5) Marsha A Chandler PhD (i)
(ii)		 414,116
0 		0
0 		52,068
0 		31,850
0 		1,470
0 		499,504
0 		0
0
(6) Julia A Miller JD (i)
(ii)		 248,850
0 		0
0 		846
0 		0
0 		15,664
0 		265,360
0 		0
0
(7) Kim E Witmer (i)
(ii)		 321,593
0 		0
0 		31,779
0 		31,850
0 		15,664
0 		400,886
0 		0
0
(8) Fred H Gage PhD (i)
(ii)		 307,674
0 		0
0 		4,530
0 		31,850
0 		12,131
0 		356,185
0 		0
0
(9) Rebecca R Newman (i)
(ii)		 294,824
0 		0
0 		36,906
0 		31,850
0 		8,376
0 		371,956
0 		0
0
(10) Dennis D O'Leary PhD (i)
(ii)		 264,316
0 		0
0 		42,034
0 		31,850
0 		15,664
0 		353,864
0 		0
0
(11) Wylie W Vale PHD (i)
(ii)		 316,957
0 		0
0 		15,378
0 		31,850
0 		12,131
0 		376,316
0 		0
0
(12) Inder Verma PhD (i)
(ii)		 332,674
0 		0
0 		27,772
0 		31,850
0 		12,131
0 		404,427
0 		0
0




Schedule J (Form 990) 2011

Schedule J (Form 990) 2011
Page 3
Part III
Supplemental Information
Complete this part to provide the information, explanation, or descriptions required for Part I, lines 1a, 1b, 3, 4c, 5a, 5b, 6a, 6b, 7, and 8. Also complete this part for any additional information.
Identifier Return Reference Explanation
QUESTIONS REGARDING COMPENSATION PART I, LINE 1A FIRST-CLASS OR CHARTER TRAVEL: DENNIS O'LEARY, PROFESSOR - $1,238; NOT TAXABLE - ACCOUNTABLE PLAN.
QUESTIONS REGARDING HOUSING ALLOWANCE OR RESIDENCE PART I, LINE 1A A HOUSING ALLOWANCE IS PROVIDED AND REPORTED AS TAXABLE COMPENSATION.
SUPPLEMENTAL NONQUALIFIED RETIREMENT PLAN PART I, LINE 4B DEFERRED COMPENSATION PLAN (SECTION 457(F)) WAS ESTABLISHED FOR THE PRESIDENT. THE INSTITUTE'S CONTRIBUTION TO THE PLAN AND THE EARNINGS FROM THE CONTRIBUTION WILL BECOME 100% VESTED UPON THE PRESIDENT'S COMPLETION OF 5 YEARS OF SERVICE. NO PAYOUTS FROM THE PLAN WERE MADE DURING THE YEAR.
NON-FIXED PAYMENTS PART I, LINE 7 WYLIE VALE - $3,500 FOR LICENSING CONSULTING. NON-FIXED PAYMENTS INCLUDE BOARD OF TRUSTEE AWARDS WHICH ARE REPORTED UNDER OTHER REPORTABLE COMPENSATION. THE BOARD OF TRUSTEE AWARDS ARE NON-BASE RECOGNITION AWARDS FOR CERTAIN LISTED INDIVIDUAL, AS APPROVED BY THE EXECUTIVE COMMITTEE OF THE BOARD OF TRUSTEES. NON-BASE RECOGNITION AWARDS ARE INCLUDED IN THE TOTAL COMPENSATION PACKAGES SUBJECT TO THE REVIEW PROCESS DESCRIBED IN SCHEDULE O FOR FORM 990, PART VI, SECTION B, LINE 15B.
Schedule J (Form 990) 2011

Additional Data


Software ID:  
Software Version:  
Schedule K
(Form 990)
Department of the Treasury
Internal Revenue Service
Supplemental Information on Tax Exempt Bonds
SchKMediumBullet Complete if the organization answered "Yes" to Form 990, Part IV, line 24a. Provide descriptions,
explanations, and any additional information in Part VI.
SchKMediumBullet Attach to Form 990. SchKMediumBullet See separate instructions.
OMB No. 1545-0047
2011
Open to Public
Inspection
Name of the organization
The Salk Institute for Biological Studies
 
Employer identification number
95-2160097
Part I
Bond Issues
(a) Issuer Name (b) Issuer EIN (c) CUSIP # (d) Date Issued (e) Issue Price (f) Description of Purpose (g) Defeased (h) On
Behalf of
Issuer 		(i) Pool
financing
Yes No Yes No Yes No
A CA STATEWIDE COMM DEV AUTHORITY
  		68-0164610 130911S92 08-11-2005 25,712,839 REFUND 03/30/94 ISSUE   X   X   X
B COUNTY OF SAN DIEGO
  		95-6000934 797391R50 05-27-2010 37,207,949 REFUND 04/13/00 ISSUE;RENOVATE/EQU   X   X   X
Part II
Proceeds
A B C D
1 Amount of bonds retired . . . . . . . . . . . . . 6,250,000 360,000    
2 Amount of bonds legally defeased . . . . . . . . . . 0 0    
3 Total proceeds of issue . . . . . . . . . . . . . 25,712,839 37,207,949    
4 Gross proceeds in reserve funds . . . . . . . . 0 0    
5 Capitalized interest from proceeds . . . . . . . . . . 0 0    
6 Proceeds in refunding escrows . . . . . . . . . . . 0 0    
7 Issuance costs from proceeds . . . . . . . . . . . 686,939 523,682    
8 Credit enhancement from proceeds . . . . . . . . . . 0 0    
9 Working capital expenditures from proceeds . . . . . . . 0 0    
10 Capital expenditures from proceeds . . . . . . . . . . 0 23,537,429    
11 Other spent proceeds . . . . . . . . . . . 0 0    
12 Other unspent proceeds . . . . . . . . . . . 0 0    
13 Year of substantial completion . . . . . . . . . . . 2012 2012
Yes No Yes No Yes No Yes No
14 Were the bonds issued as part of a current refunding issue? . . . . X   X          
15 Were the bonds issued as part of an advance refunding issue? . . . .   X   X        
16 Has the final allocation of proceeds been made? . . . . . . X   X          
17 Does the organization maintain adequate books and records to support the final allocation of proceeds? . . . . . . . . . . . . . X   X          
Part III
Private Business Use
A B C D
Yes No Yes No Yes No Yes No
1 Was the organization a partner in a partnership, or a member of an LLC, which owned property financed by tax-exempt bonds? . . . . . . .   X   X        
2 Are there any lease arrangements that may result in private business use of bond-financed property? . . . . . . . . . X   X          
For Privacy Act and Paperwork Reduction Act Notice, see the Instructions for Form 990.
Cat. No. 50193E
Schedule K (Form 990) 2011
Schedule K (Form 990) 2011
Page 2
Part III
Private Business Use (Continued)
A B C D
Yes No Yes No Yes No Yes No
3a Are there any management or service contracts that may result in private business use of bond-financed property? . . . . . . . . .   X   X        
b If ‘Yes’ to line 3a, does the organization routinely engage bond counsel or other outside counsel to review any management or service contracts relating to the financed property? . . . . .                
c Are there any research agreements that may result in private business use of bond-financed property? . . . . . . .   X   X        
d If ‘Yes’ to line 3c, does the organization routinely engage bond counsel or other outside counsel to review any research agreements relating to the financed property? .                
4 Enter the percentage of financed property used in a private business use by entities other than a section 501(c)(3) organization or a state or local government . . SchKMediumBullet 0.00000% 0.00000%   %   %
5 Enter the percentage of financed property used in a private business use as a result of unrelated trade or business activity carried on by your organization, another section 501(c)(3) organization, or a state or local government . . . . . . . SchKMediumBullet 0.00000% 0.00000%   %   %
6 Total of lines 4 and 5 . . .. . . . . . . . . 0.00000% 0.00000%   %   %
7 Does the bond issue meet the private security or payment test? . . . X   X          
8 Has the organization established written procedures to ensure that all nonqualified bonds of the issue are remediated in accordance with the requirements under
Regulations sections 1.141-12 and 1.145-2?
X   X          
Part IV
Arbitrage
A B C D
Yes No Yes No Yes No Yes No
1 Has a Form 8038-T, Arbitrage Rebate, Yield Reduction and Penalty in Lieu of Arbitrage Rebate, been filed with respect to the bond issue? . . .   X   X        
2 Is the bond issue a variable rate issue?   X   X        
3a Has the organization or the governmental issuer entered into a qualified hedge with respect to the bond issue?   X   X        
b Name of provider . . . . . . . . 0
  		0
  		 
  		 
 
c Term of hedge . . . . . . . .        
d Was the hedge superintegrated? . . . .                
e Was a hedge terminated? . . . . .                
4a Were gross proceeds invested in a guaranteed investment contract (GIC)? . . . . . .   X   X        
b Name of provider . . . . . . 0
  		0
  		 
  		 
 
c Term of GIC . . . . . . .        
d Was the regulatory safe harbor for establishing the fair market value of the GIC satisfied? . . . . . .                
5 Were any gross proceeds invested beyond an available temporary period? . . . . . .   X   X        
6 Did the bond issue qualify for an exception to rebate? . X   X          
7 Has the organization established written procedures to monitor the requirements of section 148? . . . X   X          
Schedule K (Form 990) 2011

Schedule K (Form 990) 2011
Page 3
Part V
Procedures To Undertake Corrective Action
Has the organization established written procedures to ensure that violations of federal tax requirements are timely identified and corrected through the voluntary closing agreement program if self-remediation is not available under applicable regulations? . . . . . . . . . . . . . .
Part VI
Supplemental Information
Complete this part to provide additional information for responses to questions on Schedule K (see instructions).
Identifier Return Reference Explanation
Schedule K (Form 990) 2011

Additional Data


Software ID:  
Software Version:  

Schedule L
(Form 990 or 990-EZ)
Department of the Treasury
Internal Revenue Service
Transactions with Interested Persons
MediumBullet Complete if the organization answered
"Yes" on Form 990, Part IV, lines 25a, 25b, 26, 27, 28a, 28b, or 28c,
or Form 990-EZ, Part V lines 38a or 40b.
MediumBullet Attach to Form 990 or Form 990-EZ. MediumBulletSee separate instructions.
OMB No. 1545-0047
2011
Open to Public Inspection
Name of the organization
The Salk Institute for Biological Studies
 
Employer identification number

95-2160097
Part I
Excess Benefit Transactions (section 501(c)(3) and section 501 (c)(4) organizations only).
Complete if the organization answered "Yes" on Form 990, Part IV, line 25a or 25b, or Form 990-EZ, Part V, line 40b.
1(a) Name of disqualified person (b) Description of transaction (c) Corrected?
Yes No





2
Enter the amount of tax imposed on the organization managers or disqualified persons during the year under section 4958. ......................... Bullet Image$
 
3
Enter the amount of tax, if any, on line 2, above, reimbursed by the organization ....... Bullet Image$
 

Part II
Loans to and/or From Interested Persons.
Complete if the organization answered "Yes" on Form 990, Part IV, line 26, or Form 990-EZ, Part V, line 38a.
(a) Name of interested person and purpose (b) Loan to or from the organization? (c)Original principal amount (d)Balance due (e) In default? (f) Approved by board or committee? (g)Written agreement?
To From Yes No Yes No Yes No
(1) DENNIS O'LEARY
HOME LOAN 		  X 165,000 148,500   No Yes   Yes  
Total ...............Small Bullet $ 148,500
Part III
Grants or Assistance Benefitting Interested Persons.
Complete if the organization answered "Yes" on Form 990, Part IV, line 27.
(a) Name of interested person (b)Relationship between interested person and the organization (c)Amount of grant or type of assistance
For Privacy Act and Paperwork Reduction Act Notice, see the
Instructions for Form 990 or 990-EZ.
Cat. No. 50056A
Schedule L (Form 990 or 990-EZ) 2011
Schedule L (Form 990 or 990-EZ) 2011
Page 2
Part IV
Business Transactions Involving Interested Persons.
Complete if the organization answered "Yes" on Form 990, Part IV, line 28a, 28b, or 28c.
(a) Name of interested person (b) Relationship between interested person and the organization (c) Amount of transaction (d) Description of transaction (e) Sharing of organization's revenues?
Yes No
Part V
Supplemental Information
Complete this part to provide additional information for responses to questions on Schedule L (see instructions).
Identifier Return Reference Explanation
Schedule L (Form 990 or 990-EZ) 2011

Additional Data


Software ID:  
Software Version:  




SCHEDULE M
(Form 990)

Department of the Treasury
Internal Revenue Service
NonCash Contributions
Right pointing arrow large imageComplete if the organization answered "Yes" on Form 990, Part IV, lines 29 or 30.
Right pointing arrow large image Attach to Form 990.
OMB No. 1545-0047
2011
Open to Public Inspection
Name of the organization
The Salk Institute for Biological Studies
 
Employer identification number

95-2160097
Part I
Types of Property
(a)
Check if applicable 		(b)
Number of Contributions or items contributed 		(c)
Noncash contribution amounts reported on
Form 990, Part VIII, line 1g 		(d)
Method of determining
noncash contribution amounts
1 Art—Works of art ....        
2 Art—Historical treasures .        
3 Art—Fractional interests ..        
4 Books and publications ..      
5 Clothing and household
goods ....... 		     
6 Cars and other vehicles ..        
7 Boats and planes ....        
8 Intellectual property ...        
9 Securities—Publicly traded . X 19 3,558,046 MARKET VALUE
10 Securities—Closely held stock .        
11 Securities—Partnership, LLC,
or trust interests .... 		       
12 Securities—Miscellaneous ..        
13 Qualified conservation
contribution—Historic
structures ..... 		       
14 Qualified conservation
contribution—Other ... 		       
15 Real estate—Residential .        
16 Real estate—Commercial ..        
17 Real estate—Other ...        
18 Collectibles .....        
19 Food inventory ...        
20 Drugs and medical supplies .        
21 Taxidermy ......        
22 Historical artifacts ....        
23 Scientific specimens ..        
24 Archeological artifacts ...        
25 Other Right pointing arrow large image ( )
26 Other Right pointing arrow large image( )
27 Other Right pointing arrow large image( )
28 Other Right pointing arrow large image ( )
29
Number of Forms 8283 received by the organization during the tax year for contributions
for which the organization completed Form 8283, Part IV, Donee Acknowledgement ...
29
 
Yes
No
30a
During the year, did the organization receive by contribution any property reported in Part I, lines 1-28 that it
must hold for at least three years from the date of the initial contribution, and which is not required to be used
for exempt purposes for the entire holding period? ..................
30a
 
No
b
If "Yes," describe the arrangement in Part II.
31
Does the organization have a gift acceptance policy that requires the review of any non-standard contributions?
31
Yes
 
32a
Does the organization hire or use third parties or related organizations to solicit, process, or sell noncash
contributions? ............................
32a
 
No
b
If "Yes," describe in Part II.
33
If the organization did not report revenues in column (c) for a type of property for which column (a) is checked,
describe in Part II.
For Privacy Act and Paperwork Reduction Act Notice, see the Instructions for Form 990.
Cat. No. 51227J
Schedule M (Form 990) 2011
Schedule M (Form 990) 2011
Page 2
Part II
Supplemental Information. Complete this part to provide the information required by Part I, lines 30b,
32b, and 33 and whether the organization is reporting in Part I, column (b) the number of contributions, the number of items received, or a combination of both. Also complete this part for any additional information.
Identifier Return Reference Explanation
Schedule M (Form 990) 2011
Additional Data


Software ID:  
Software Version:  
SCHEDULE O
(Form 990 or 990-EZ)

Department of the Treasury
Internal Revenue Service
Supplemental Information to Form 990 or 990-EZ

Complete to provide information for responses to specific questions on
Form 990 or to provide any additional information.
MediumBullet Attach to Form 990 or 990-EZ.
OMB No. 1545-0047
2011
Open to Public
Inspection
Name of the organization
The Salk Institute for Biological Studies
 
Employer identification number

95-2160097
Identifier Return Reference Explanation
GOVERNING BODY AND MANAGEMENT FORM 990, PART VI, SECTION A, LINES 1a, 6, 7a, 7b LINE 1A: THE EXECUTIVE COMMITTEE SHALL ADVISE AND AID THE OFFICERS OF THE CORPORATION IN ALL MATTERS CONCERNING ITS INTERESTS, INCLUDING WITHOUT LIMITATION ALL MATTERS RELATING TO COMPENSATION AND BENEFITS, AND SHALL POSSESS AND MAY EXERCISE, DURING THE INTERVALS BETWEEN THE MEETINGS OF THE BOARD OF TRUSTEES, ALL THE POWERS AND AUTHORITY OF THE BOARD OF TRUSTEES IN THE MANAGEMENT OF THE BUSINESS AND AFFAIRS OF THE CORPORATION, INCLUDING THE POWER TO AUTHORIZE THE CORPORATE SEAL TO BE AFFIXED TO ANY AND ALL DOCUMENTS WHICH MAY REQUIRE THE SAME TO BE AFFIXED THERETO, INSOFAR AS SUCH SEEMS TO THE EXECUTIVE COMMITTEE FOR THE BEST INTERESTS OF THE CORPORATION, IN ALL CASES IN WHICH SPECIFIC DIRECTIONS SHALL NOT HAVE BEEN GIVEN BY THE BOARD OF TRUSTEES, EXCEPT THAT THE EXECUTIVE COMMITTE SHALL HAVE NO POWER TO ADOPT, AMEND, OR REPEAL THE BY-LAWS. LINE 6: MEMBERSHIP OF THE CORPORATION CONSISTS OF THE PERSONS ELECTED TO THE BOARD OF TRUSTEES AND THREE MEMBERS FROM AMONG THE RESIDENT AND NON-RESIDENT FELLOWS AND PROFESSORS CHOSEN AND ELECTED ANNUALLY BY THE RESIDENT AND NON-RESIDENT FELLOWS AND PROFESSORS. LINE 7a: THE MEMBERS OF THE CORPORATION ELECT THE TRUSTEES. LINE 7b: THE MEMBERS OF THE CORPORATION MAY ALTER, AMEND, OR REPEAL THE BY-LAWS BY VOTE.
POLICIES FORM 990, PART VI, SECTION B, LINES 11B, 12C AND 15A/B LINE 11B: THE FORM 990 IS PREPARED BY THE INSTITUTE, INTERNALLY REVIEWED BY THE SR. DIRECTOR OF FINANCE AND THE CHIEF FINANCIAL OFFICER AND EXTERNALLY REVIEWED BY THE TAX DEPARTMENT OF A PUBLIC ACCOUNTING FIRM. A COPY OF THE PREPARED FORM 990 IS PROVIDED TO ALL BOARD MEMBERS AND THE AUDIT COMMITTEE FOR REVIEW AND DISCUSSION PRIOR TO ELECTRONIC FILING. LINE 12C: ANNUALLY, THE CONFLICT OF INTEREST DISCLOSURE STATEMENT IS SENT OUT FOR COMPLETION BY THE MEMBERS OF THE BOARD OF TRUSTEES, SENIOR MEMBERS OF ADMINISTRATION AND RESEARCHERS. THE DESIGNATED OFFICIAL FOR EACH GROUP REVIEWS THE COMPLETED FORMS AND BRINGS ANY POTENTIAL CONFLICT OF INTEREST TO THE RESPECTIVE COMMITTEES FOR REVIEW. UPON DETERMINATION THAT A CONFLICT OF INTEREST EXISTS, THE FOLLOWING CONDITIONS OR RESTRICTIONS MAY BE IMPOSED: A. MONITORING OF ACTIVITIES GENERATING THE CONFLICT BY ANOTHER MEMBER; B. DISQUALIFICATION FROM PARTICIPATION IN THE ACTIVITIES GIVING RISE TO THE CONFLICT; C. MODIFICATION OF RESPONSIBILITIES TO AVOID CONFLICTS; D. PUBLIC DISCLOSURE OR DIVESTITURE OF SIGNIFICANT FINANCIAL INTERESTS; E. MODIFICATION OF THE RESEARCH PLAN OR REMOVAL OF THE AFFECTED RESEARCHER FROM THE RESEARCH; F. SEVERANCE OF RELATIONSHIP THAT CREATES ACTUAL OR POTENTIAL CONFLICTS; G. TERMINATION OF EMPLOYMENT. LINE 15A/B:AN INDEPENDENT CONSULTANT WAS RETAINED BY THE SALK INSTITUTE TO ADVISE ON COMPENSATION ISSUES. MARKET ANALYSIS ON THE COMPETITIVENESS OF THE BASE SALARY AND TOTAL COMPENSATION (INCLUDING BENEFITS) FOR THE CEO, EVP, AND CFO WERE CONDUCTED IN 2010. THE INDEPENDENT CONSULTANT EVALUATED TOTAL COMPENSATION COMPARED TO LIKE ROLES AMOUNT ORGANIZATIONS PROVIDING SUBSTANTIALLY SIMILAR SERVICES IN THE RESEARCH INDUSTRY, INCLUDING BOTH FOR-PROFIT AND NOT-FOR-PROFIT ORGANIZATIONS. THE CONSULTANT CONSIDERED THE SIZE AND SCOPE OF OPERATIONS OF THE INCUMBENTS. THE CONSULTANT GAVE THE OPINION THAT THE TOTAL COMPENSATION FALLS WELL WITHIN REASONABLE RANGE OF COMPETITIVE PRACTICES. THE CONSULTANT'S REPORTS WERE REVIEWED BY THE EXECUTIVE COMMITTEE WHICH SERVED AS THE COMPENSATION COMMITTEE, EXCLUDING PERSONS WITH A CONFLICT OF INTEREST WITH RESPECT TO THE COMPENSATION ARRANGEMENT. DOCUMENTATION AND RECORDKEEPING WITH RESPECT TO THE DELIBERATIONS AND DECISIONS REGARDING THE COMPENSATION PACKAGE WERE INCLUDED IN THE MINUTES OF THE EXECUTIVE COMMITTEE MEETING. A COPY OF THE CONSULTANT'S REPORTS WAS ATTACHED TO THE MINUTES OF THE MEETING. IN 2011, FOR 2012 CALENDAR YEAR COMPENSATION ACTIONS, AN INDEPENDENT CONSULTANT PROVIDED AN UPDATE TO THE 2010 ANNUAL REVIEW AND PROVIDED RECOMMENDATIONS ON 2012 COMPENSATION ACTIONS, AS APPROPRIATE. THE CONSULTANT GAVE THE OPINION THAT THE SALK'S EXECUTIVE CASH COMPENSATION PROGRAM CONTINUES TO BE BALANCED IN DESIGN, ALIGNED WITH THE SALK'S MISSION AND VALUES, AND REASONABLE IN AMOUNT. THE CONSULTANT'S REPORTS WERE REVIEWED BY THE EXECUTIVE COMMITTEE OF THE BOARD OF TRUSTEES WHICH SERVED AS THE COMPENSATION COMMITTEE, EXCLUDING PERSONS WITH A CONFLICT OF INTEREST WITH RESPECT TO THE COMPENSATION ARRANGEMENT. DOCUMENTATION AND RECORDKEEPING WITH RESPECT TO THE DELIBERATIONS AND DECISIONS REGARDING THE COMPENSATION PACKAGE WERE INCLUDED IN THE MINUTES OF THE EXECUTIVE COMMITTEE MEETING. A COPY OF THE CONSULTANT'S REPORTS WAS ATTACHED TO THE MINUTES OF THE MEETING.
DISCLOSURE FORM 990, PART VI, SECTION C, LINE 19 UPON REQUEST, THE OFFICE OF THE CHIEF FINANCIAL OFFICER MAKES AVAILABLE TO THE PUBLIC ITS GOVERNING DOCUMENTS AND CONFLICT OF INTEREST POLICY. FINANCIAL STATEMENTS ARE AVAILABLE ON THE SALK WEB SITE.
OTHER CHANGES IN NET ASSETS FORM 990, PART XI, LINE 5 UNREALIZED INVESTMENT LOSSES IN EXCESS OF AMOUNT DESIGNATED FOR CURRENT OPERATIONS - ($8,223,913); POSTRETIREMENT BENEFIT CHANGES OTHER THAN NET PERIODIC BENEFIT COST - ($46,931); ROUNDING - $2
COMPENSATION OF DIRECTORS PART VII, DIRECTORS COMPENSATION THE FOLLOWING INDIVIDUALS WERE COMPENSATED FOR THE FOLLOWING SERVICES AND NOT PAID AS TRUSTEES: GEOFFREY M. WAHL, PH.D. - PROFESSOR THOMAS D. ALBRIGHT, PH.D. - PROFESSOR CHRISTOPHER R. KINTNER, PH.D. - PROFESSOR
For Paperwork Reduction Act Notice, see the Instructions for Form 990 or 990-EZ.
Cat. No. 51056K
Schedule O (Form 990 or 990-EZ) 2011

Additional Data


Software ID:  
Software Version:  
SCHEDULE R
(Form 990)
Department of the Treasury
Internal Revenue Service
Related Organizations and Unrelated Partnerships
MediumBulletComplete if the organization answered "Yes" to Form 990, Part IV, line 33, 34, 35, 36, or 37.
MediumBulletAttach to Form 990. MediumBullet See separate instructions.

OMB No. 1545-0047
2011
Open to Public Inspection
Name of the organization
The Salk Institute for Biological Studies
 
Employer identification number

95-2160097
Part I
Identification of Disregarded Entities (Complete if the organization answered "Yes" on Form 990, Part IV, line 33.)
(a)
Name, address, and EIN of disregarded entity


(b)
Primary activity


 		(c)
Legal domicile (state
or foreign country)

 		(d)
Total income
(e)
End-of-year assets


 		(f)
Direct controlling
entity

















Part II
Identification of Related Tax-Exempt Organizations (Complete if the organization answered "Yes" on Form 990, Part IV, line 34 because it had one or more related tax-exempt organizations during the tax year.)
(a)
Name, address, and EIN of related organization


(b)
Primary activity


 		(c)
Legal domicile (state
or foreign country)

 		(d)
Exempt Code section
(e)
Public charity status
(if section 501(c)(3))

 		(f)
Direct controlling
entity

 		(g)
Section 512(b)(13) controlled organization
Yes No
(1) LA JOLLA BIOLOGICAL LABORATORIES

PO BOX 85800 - FINANCE

SAN DIEGO,CA92186
95-3655649 		Research CA 501(C)(3) 11-I NA
 
 
No












For Privacy Act and Paperwork Reduction Act Notice, see the Instructions for Form 990.
Cat. No. 50135Y
Schedule R (Form 990) 2011
Schedule R (Form 990) 2011
Page 2
Part III
Identification of Related Organizations Taxable as a Partnership (Complete if the organization answered "Yes" on Form 990, Part IV, line 34 because it had one or more related organizations treated as a partnership during the tax year.)
(a)
Name, address, and EIN of
related organization



 		(b)
Primary activity




 		(c)
Legal
domicile
(state or foreign
country)


 		(d)
Direct controlling
entity



 		(e)
Predominant income(related, unrelated, excluded from tax under sections 512-514)

(f)
Share of total income




 		(g)
Share of end-of-year
assets



 		(h)
Disproprtionate allocations?




 		(i)
Code V—UBI
amount in box 20 of
Schedule K-1
(Form 1065)
 		(j)
General or
managing
partner?



 		(k)
Percentage
ownership
Yes No Yes No












Part IV
Identification of Related Organizations Taxable as a Corporation or Trust (Complete if the organization answered "Yes" on Form 990, Part IV, line 34 because it had one or more related organizations treated as a corporation or trust during the tax year.)
(a)
Name, address, and EIN of related organization



 		(b)
Primary activity



 		(c)
Legal domicile
(state or
foreign
country)
 		(d)
Direct controlling
entity


 		(e)
Type of entity
(C corp, S corp,
or trust)

 		(f)
Share of total income



 		(g)
Share of
end-of-year
assets

 		(h)
Percentage
ownership
(1) SALK INSTITUTE COMMERCIAL SERVICES CORP
PO BOX 85800 - FINANCE
SAN DIEGO,CA921865800
23-2159172 		MGMT SERVICES PA SALK INSTITUTE
  		C 132 54,566 100.000 %












Schedule R (Form 990) 2011
Schedule R (Form 990) 2011
Page 3
Part V
Transactions With Related Organizations (Complete if the organization answered "Yes" on Form 990, Part IV, line 34, 35, 35A, or 36.)
Note. Complete line 1 if any entity is listed in Parts II, III or IV.
Yes
No
1 During the tax year, did the orgranization engage in any of the following transactions with one or more related organizations listed in Parts II-IV?
a Receipt of (i) interest (ii) annuities (iii) royalties (iv) rent from a controlled entity . . . . . . . . . . . . . . . . . . . . . . .
1a
 
No
b Gift, grant, or capital contribution to related organization(s) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1b
 
No
c Gift, grant, or capital contribution from related organization(s) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1c
 
No
d Loans or loan guarantees to or for related organization(s) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1d
 
No
e Loans or loan guarantees by related organization(s) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1e
 
No
f Sale of assets to related organization(s) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1f
 
No
g Purchase of assets from related organization(s) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1g
 
No
h Exchange of assets with related organization(s) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1h
 
No
i Lease of facilities, equipment, or other assets to related organization(s) . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1i
 
No
j Lease of facilities, equipment, or other assets from related organization(s) . . . . . . . . . . . . . . . . . . . . . . . . . . .
1j
 
No
k Performance of services or membership or fundraising solicitations for related organization(s) . . . . . . . . . . . . . . . . . . . .
1k
 
No
l Performance of services or membership or fundraising solicitations by related organization(s) . . . . . . . . . . . . . . . . . . . .
1l
 
No
m Sharing of facilities, equipment, mailing lists, or other assets with related organization(s) . . . . . . . . . . . . . . . . . . . . .
1m
Yes
 
n Sharing of paid employees with related organization(s) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1n
Yes
 
o Reimbursement paid to related organization(s) for expenses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1o
 
No
p Reimbursement paid by related organization(s) for expenses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1p
Yes
 
q Other transfer of cash or property to related organization(s) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1q
 
No
r Other transfer of cash or property from related organization(s) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1r
 
No
2
If the answer to any of the above is "Yes," see the instructions for information on who must complete this line, including covered relationships and transaction thresholds.
(a)
Name of other organization 		(b)
Transaction
type(a-r) 		(c)
Amount involved 		(d)
Method of determining amount involved
(1)
(2)
(3)
(4)
(5)
(6)
Schedule R (Form 990) 2011
Schedule R (Form 990) 2011
Page 4
Part VI
Unrelated Organizations Taxable as a Partnership (Complete if the organization answered "Yes" on Form 990, Part IV, line 37.)
Provide the following information for each entity taxed as a partnership through which the organization conducted more than five percent of its activities (measured by total assets or gross revenue) that was not a related organization. See instructions regarding exclusion for certain investment partnerships.
(a)
Name, address, and EIN of entity 		(b)
Primary activity 		(c)
Legal domicile
(state or foreign
country) 		(d)
Predominant income(related, unrelated, excluded from tax under sections 512-514)

(e)
Are all
partners
section
501(c)(3)
organizations? 		(f)
Share of total income




 		(g)
Share of
end-of-year
assets 		(h)
Disproprtionate allocations? 		(i)
Code V—UBI
amount in box
20 of Schedule K-1
(Form 1065) 		(j)
General or
managing
partner? 		(k)
Percentage
ownership
Yes No Yes No Yes No






























Schedule R (Form 990) 2011
Schedule R (Form 990) 2011
Page 5
Part VII
Supplemental Information
Complete this part to provide additional information for responses to questions on Schedule R (see instructions).
Identifier Return Reference Explanation
Additional Data


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