Form990-PF

Department of the Treasury
Internal Revenue Service
Return of Private Foundation
or Section 4947(a)(1) Nonexempt Charitable Trust
Treated as a Private Foundation
Note. The foundation may be able to use a copy of this return to satisfy state reporting requirements.
OMB No. 1545-0052
2012
Open to Public Inspection
For calendar year 2012, or tax year beginning 10-01-2012 , and ending 09-30-2013
Name of foundation
THE CLAY MATHEMATICS INSTITUTE INC
 
% THE CORPORATION
Number and street (or P.O. box number if mail is not delivered to street address)10 Memorial BlvdSuite 902Room/suite
City or town, state, and ZIP code
Providence, RI02903
A Employer identification number

13-4025978
B Telephone number (see instructions)

(401) 490-0700
C bullet
G Check all that apply:

D 1. bullet
2. bullet
H Check type of organization:
I Fair market value of all assets at end
of year (from Part II, col. (c),
line 16)bullet$69,270,772J Accounting method:
 
(Part I, column (d) must be on cash basis.)
E bullet
F bullet
Part I Analysis of Revenue and Expenses (The total of amounts in columns (b), (c), and (d) may not necessarily equal the amounts in column (a) (see instructions).) (a) Revenue and
expenses per
books 		(b) Net investment
income 		(c) Adjusted net
income 		(d) Disbursements
for charitable
purposes
(cash basis only)
Revenue 1 Contributions, gifts, grants, etc., received (attach schedule) 0
2 Check bullet
3 Interest on savings and temporary cash investments 12,438 12,438 12,438
4 Dividends and interest from securities...... 455,816 455,816 455,816
5a Gross rents..............      
b Net rental income or (loss)  
6a Net gain or (loss) from sale of assets not on line 10 8,783,226
b Gross sales price for all assets on line 6a 10,578,469
7 Capital gain net income (from Part IV, line 2)... 8,783,226
8 Net short-term capital gain.........  
9 Income modifications...........  
10a Gross sales less returns and allowances 2,373
b Less: Cost of goods sold....  
c Gross profit or (loss) (attach schedule)..... Click to see attachment 2,373 2,373
11 Other income (attach schedule)....... Click to see attachment 2,395 0 2,395
12 Total. Add lines 1 through 11........ 9,256,248 9,251,480 473,022
Operating and Administrative Expenses 13 Compensation of officers, directors, trustees, etc. 283,092 0 0 283,092
14 Other employee salaries and wages...... 550,333 0 0 550,333
15 Pension plans, employee benefits....... 64,594 0 0 64,594
16a Legal fees (attach schedule)......... Click to see attachment 48,115 0 0 48,115
b Accounting fees (attach schedule)....... Click to see attachment 64,270 0 0 64,270
c Other professional fees (attach schedule).... Click to see attachment 297,125 190,110 0 107,015
17 Interest...............        
18 Taxes (attach schedule) (see instructions) Click to see attachment 267,029 0 0 90,029
19 Depreciation (attach schedule) and depletion... Click to see attachment 26,921    
20 Occupancy.............. 70,283 0 0 70,283
21 Travel, conferences, and meetings....... 223,439 0 0 223,439
22 Printing and publications.......... 18,738 0 0 18,738
23 Other expenses (attach schedule)....... Click to see attachment 137,519 1,291 0 136,228
24 Total operating and administrative expenses.
Add lines 13 through 23.......... 2,051,458 191,401 0 1,656,136
25 Contributions, gifts, grants paid........ 35,000 35,000
26 Total expenses and disbursements. Add lines 24 and 25 2,086,458 191,401 0 1,691,136
27 Subtract line 26 from line 12:
a Excess of revenue over expenses and disbursements 7,169,790
b Net investment income (if negative, enter -0-) 9,060,079
c Adjusted net income (if negative, enter -0-)... 473,022
For Paperwork Reduction Act Notice, see instructions.
Cat. No. 11289X Form 990-PF (2012)
Form 990-PF (2012)
Page 2
Part II Balance Sheets Attached schedules and amounts in the description column
should be for end-of-year amounts only. (See instructions.)		 Beginning of year End of year
(a) Book Value (b) Book Value (c) Fair Market Value
Assets 1 Cash—non-interest-bearing............... 250,068 282,876 282,876
2 Savings and temporary cash investments.......... 14,918,320 23,089,961 23,089,961
3 Accounts receivable bullet  
Less: allowance for doubtful accounts bullet        
4 Pledges receivable bullet  
Less: allowance for doubtful accounts bullet        
5 Grants receivable.................      
6 Receivables due from officers, directors, trustees, and other
disqualified persons (attach schedule) (see page 15 of the
instructions)....................      
7 Other notes and loans receivable (attach schedule) bullet  
Less: allowance for doubtful accounts bullet        
8 Inventories for sale or use...............      
9 Prepaid expenses and deferred charges...........      
10a Investments—U.S. and state government obligations (attach schedule)      
b Investments—corporate stock (attach schedule)........ 62,450,777 Click to see attachment45,863,609 45,863,609
c Investments—corporate bonds (attach schedule)........      
11 Investments—land, buildings, and equipment: basis bullet1,273,294
Less: accumulated depreciation (attach schedule) bullet1,238,968 21,922 34,326 34,326
12 Investments—mortgage loans..............      
13 Investments—other (attach schedule)...........      
14 Land, buildings, and equipment: basis bullet  
Less: accumulated depreciation (attach schedule) bullet        
15 Other assets (describe bullet)      
16 Total assets (to be completed by all filers—see the
instructions. Also, see page 1, item I) 77,641,087 69,270,772 69,270,772
Liabilities 17 Accounts payable and accrued expenses..........    
18 Grants payable...................    
19 Deferred revenue..................    
20 Loans from officers, directors, trustees, and other disqualified persons    
21 Mortgages and other notes payable (attach schedule)......    
22 Other liabilities (describe bullet) Click to see attachment0 Click to see attachment36,617
23 Total liabilities (add lines 17 through 22).......... 0 36,617
Net Assets or Fund Balances bullet
and complete lines 24 through 26 and lines 30 and 31.
24 Unrestricted.................... 77,641,087 69,234,155
25 Temporarily restricted................    
26 Permanently restricted................    
bullet
and complete lines 27 through 31.
27 Capital stock, trust principal, or current funds.........    
28 Paid-in or capital surplus, or land, bldg., and equipment fund    
29 Retained earnings, accumulated income, endowment, or other funds    
30 Total net assets or fund balances (see page 17 of the
instructions).................... 77,641,087 69,234,155
31 Total liabilities and net assets/fund balances (see page 17 of
the instructions).................. 77,641,087 69,270,772
Part III Analysis of Changes in Net Assets or Fund Balances
1 Total net assets or fund balances at beginning of year—Part II, column (a), line 30 (must agree
with end-of-year figure reported on prior year’s return)............... 1 77,641,087
2 Enter amount from Part I, line 27a..................... 2 7,169,790
3 Other increases not included in line 2 (itemize) bullet 3  
4 Add lines 1, 2, and 3.......................... 4 84,810,877
5 Decreases not included in line 2 (itemize) bulletClick to see attachment 5 15,576,722
6 Total net assets or fund balances at end of year (line 4 minus line 5)—Part II, column (b), line 30. 6 69,234,155
Form 990-PF (2012)
Form 990-PF (2012)
Page 3
Part IV
Capital Gains and Losses for Tax on Investment Income
(a) List and describe the kind(s) of property sold (e.g., real estate,
2-story brick warehouse; or common stock, 200 shs. MLC Co.) 		(b) How acquired
P—Purchase
D—Donation 		(c) Date acquired
(mo., day, yr.) 		(d) Date sold
(mo., day, yr.)
1 a REPLIGEN CORP P    
b THROMBOGENICS NV.LEUVEN P    
c AFLAC INC P    
d
e
(e) Gross sales price (f) Depreciation allowed
(or allowable) 		(g) Cost or other basis
plus expense of sale 		(h) Gain or (loss)
(e) plus (f) minus (g)
a 335,566   199,579 135,987
b 7,414,823   510,015 6,904,808
c 2,828,080   1,085,649 1,742,431
d
e
Complete only for assets showing gain in column (h) and owned by the foundation on 12/31/69 (l) Gains (Col. (h) gain minus
col. (k), but not less than -0-) or
Losses (from col.(h))
(i) F.M.V. as of 12/31/69 (j) Adjusted basis
as of 12/31/69 		(k) Excess of col. (i)
over col. (j), if any
a       135,987
b       6,904,808
c       1,742,431
d
e
2 Capital gain net income or (net capital loss) Bracket If gain, also enter in Part I, line 7
If (loss), enter -0- in Part I, line 7		 Bracket 2 8,783,226
3 Net short-term capital gain or (loss) as defined in sections 1222(5) and (6):
If gain, also enter in Part I, line 8, column (c) (see instructions). If (loss), enter -0-
in Part I, line 8 . . . . . . . . . . . . . . . . 		Bracket 3  
Part V
Qualification Under Section 4940(e) for Reduced Tax on Net Investment Income
(For optional use by domestic private foundations subject to the section 4940(a) tax on net investment income.)

If section 4940(d)(2) applies, leave this part blank.
Was the foundation liable for the section 4942 tax on the distributable amount of any year in the base period?
If “Yes,” the foundation does not qualify under section 4940(e). Do not complete this part.
1 Enter the appropriate amount in each column for each year; see page 18 of the instructions before making any entries.
(a)
Base period years Calendar
year (or tax year beginning in) 		(b)
Adjusted qualifying distributions 		(c)
Net value of noncharitable-use assets 		(d)
Distribution ratio
(col. (b) divided by col. (c))
2011 2,777,771 65,474,741 0.042425
2010 2,502,167 66,055,877 0.03788
2009 3,474,244 62,210,371 0.055847
2008 7,180,193 54,679,718 0.131314
2007 4,276,148 77,155,599 0.055422
2 Total of line 1, column (d) ...................... 2 0.322888
3 Average distribution ratio for the 5-year base period—divide the total on line 2 by 5, or by
the number of years the foundation has been in existence if less than 5 years. . . 		3 0.064578
4 Enter the net value of noncharitable-use assets for 2012 from Part X, line 5..... 4 82,520,793
5 Multiply line 4 by line 3....................... 5 5,329,028
6 Enter 1% of net investment income (1% of Part I, line 27b)........... 6 90,601
7 Add lines 5 and 6......................... 7 5,419,629
8 Enter qualifying distributions from Part XII, line 4.............. 8 1,730,461
If line 8 is equal to or greater than line 7, check the box in Part VI, line 1b, and complete that part using a 1% tax rate. See
the Part VI instructions.
Form 990-PF (2012)
Form 990-PF (2012)
Page 4
Part VI
Excise Tax Based on Investment Income (Section 4940(a), 4940(b), 4940(e), or 4948—see page 18 of the instructions)
1a Bulletand enter “N/A” on line 1. Bracket
Date of ruling or determination letter:   (attach copy of letter if necessary–see instructions)
b 1 181,202
hereBulletand enter 1% of Part I, line 27b...................
c All other domestic foundations enter 2% of line 27b. Exempt foreign organizations enter 4% of Part I, line 12, col. (b)
2 Tax under section 511 (domestic section 4947(a)(1) trusts and taxable foundations only. Others enter -0-) 2  
3 Add lines 1 and 2............................ 3 181,202
4 Subtitle A (income) tax (domestic section 4947(a)(1) trusts and taxable foundations only. Others enter -0-). 4  
5 Tax based on investment income. Subtract line 4 from line 3. If zero or less, enter -0- ..... 5 181,202
6 Credits/Payments:
a 2012 estimated tax payments and 2011 overpayment credited to 2012 6a 183,506
b Exempt foreign organizations—tax withheld at source....... 6b
c Tax paid with application for extension of time to file (Form 8868) 6c  
d Backup withholding erroneously withheld ........... 6d  
7 Total credits and payments. Add lines 6a through 6d.............. 7 183,506
8 Enter any penalty for underpayment of estimated tax. if Form 2220 is attached. Click to see attachment 8 10
9 Tax due. If the total of lines 5 and 8 is more than line 7, enter amount owed.......Bullet 9  
10 Overpayment. If line 7 is more than the total of lines 5 and 8, enter the amount overpaid...Bullet 10 2,294
11 Enter the amount of line 10 to be: Credited to 2013 estimated taxBullet2,294 Refunded Bullet 11  
Part VII-A
Statements Regarding Activities
1a
During the tax year, did the foundation attempt to influence any national, state, or local legislation or did
Yes
No
it participate or intervene in any political campaign? ....................
1a
 
No
b
Did it spend more than $100 during the year (either directly or indirectly) for political purposes (see page 19 of
the instructions for definition)?............................
1b
 
No
If the answer is “Yes” to 1a or 1b, attach a detailed description of the activities and copies of any materials
published or distributed by the foundation in connection with the activities.
c
Did the foundation file Form 1120-POL for this year?.....................
1c
 
No
d
Enter the amount (if any) of tax on political expenditures (section 4955) imposed during the year:
(1) On the foundation. bullet$   (2) On foundation managers.bullet$  
e
Enter the reimbursement (if any) paid by the foundation during the year for political expenditure tax imposed
on foundation managers.bullet$  
2
Has the foundation engaged in any activities that have not previously been reported to the IRS?.......
2
 
No
If “Yes,” attach a detailed description of the activities.
3
Has the foundation made any changes, not previously reported to the IRS, in its governing instrument, articles
of incorporation, or bylaws, or other similar instruments? If “Yes,” attach a conformed copy of the changes....
3
 
No
4a
Did the foundation have unrelated business gross income of $1,000 or more during the year?........
4a
 
No
b
If “Yes,” has it filed a tax return on Form 990-T for this year?...................
4b
 
 
5
Was there a liquidation, termination, dissolution, or substantial contraction during the year?.........
5
 
No
If “Yes,” attach the statement required by General Instruction T.
6
Are the requirements of section 508(e) (relating to sections 4941 through 4945) satisfied either:
  • By language in the governing instrument, or
  • By state legislation that effectively amends the governing instrument so that no mandatory directions
    • that conflict with the state law remain in the governing instrument?................
    6
    Yes
     
    7
    Did the foundation have at least $5,000 in assets at any time during the year? If “Yes,” complete Part II, col. (c), and Part XV.
    7
    Yes
     
    8a
    Enter the states to which the foundation reports or with which it is registered (see instructions)
    bulletDE
    b
    If the answer is “Yes” to line 7, has the foundation furnished a copy of Form 990-PF to the Attorney
    General (or designate) of each state as required by General Instruction G? If “No,” attach explanation .
    8b
    Yes
     
    9
    Is the foundation claiming status as a private operating foundation within the meaning of section 4942(j)(3)
    or 4942(j)(5) for calendar year 2012 or the taxable year beginning in 2012 (see instructions for Part XIV)?
    If “Yes,” complete Part XIV.............................
    9
    Yes
     
    10
    Did any persons become substantial contributors during the tax year? If “Yes,” attach a schedule listing their names and addresses.
    10
     
    No
    11
    At any time during the year, did the foundation, directly or indirectly, own a controlled entity within the
    meaning of section 512(b)(13)? If "Yes," attach schedule. (see instructions) .............
    11
     
    No
    12
    Did the foundation make a distribution to a donor advised fund over which the foundation or a disqualified person had
    advisory privileges? If "Yes," attach statement (see instructions).................
    12
     
    No
    13
    Did the foundation comply with the public inspection requirements for its annual returns and exemption application?
    13
    Yes
     
    Website addressbulletclaymath.org
    14
    The books are in care ofbulletTHE CORPORATION Telephone no.bullet (401) 490-0700
    Located atbullet10 MEMORIAL BLVD SUITE 902ProvidenceRI ZIP+4bullet02903
    15
    Section 4947(a)(1) nonexempt charitable trusts filing Form 990-PF in lieu of Form 1041.........bullet
    and enter the amount of tax-exempt interest received or accrued during the year ......bullet
    15  
    16
    At any time during calendar year 2012, did the foundation have an interest in or a signature or other authority over
    a bank, securities, or other financial account in a foreign country? .................
    16
     
    No
    See instructions for exceptions and filing requirements for Form TD F 90-22.1. If "Yes", enter the name of the foreign country bullet  
    Form 990-PF (2012)
    Form 990-PF (2012)
    Page 5
    Part VII-B
    Statements Regarding Activities for Which Form 4720 May Be Required
    File Form 4720 if any item is checked in the “Yes” column, unless an exception applies.
    Yes
    No
    1a
    During the year did the foundation (either directly or indirectly):
    (1) Engage in the sale or exchange, or leasing of property with a disqualified person?
    (2) Borrow money from, lend money to, or otherwise extend credit to (or accept it from)
    a disqualified person?.........................
    (3) Furnish goods, services, or facilities to (or accept them from) a disqualified person?
    (4) Pay compensation to, or pay or reimburse the expenses of, a disqualified person?
    (5) Transfer any income or assets to a disqualified person (or make any of either available
    for the benefit or use of a disqualified person)?.................
    (6) Agree to pay money or property to a government official? (Exception. Check “No”
    if the foundation agreed to make a grant to or to employ the official for a period
    after termination of government service, if terminating within 90 days.).........
    b
    If any answer is “Yes” to 1a(1)–(6), did any of the acts fail to qualify under the exceptions described in Regulations
    section 53.4941(d)-3 or in a current notice regarding disaster assistance (see page 20 of the instructions)?...
    1b
     
    No
    .........bullet
    c
    Did the foundation engage in a prior year in any of the acts described in 1a, other than excepted acts,
    that were not corrected before the first day of the tax year beginning in 2012?.............
    1c
     
    No
    2
    Taxes on failure to distribute income (section 4942) (does not apply for years the foundation was a private
    operating foundation defined in section 4942(j)(3) or 4942(j)(5)):
    a
    At the end of tax year 2012, did the foundation have any undistributed income (lines 6d
    and 6e, Part XIII) for tax year(s) beginning before 2012?...............
    If “Yes,” list the years bullet20, 20, 20, 20
    b
    Are there any years listed in 2a for which the foundation is not applying the provisions of section 4942(a)(2)
    (relating to incorrect valuation of assets) to the year’s undistributed income? (If applying section 4942(a)(2)
    to all years listed, answer “No” and attach statement—see instructions.) ..............
    2b
     
     
    c
    If the provisions of section 4942(a)(2) are being applied to any of the years listed in 2a, list the years here.
    bullet20, 20, 20, 20
    3a
    Did the foundation hold more than a 2% direct or indirect interest in any business enterprise at
    any time during the year?.........................
    b
    If “Yes,” did it have excess business holdings in 2012 as a result of (1) any purchase by the foundation
    or disqualified persons after May 26, 1969; (2) the lapse of the 5-year period (or longer period approved
    by the Commissioner under section 4943(c)(7)) to dispose of holdings acquired by gift or bequest; or (3)
    the lapse of the 10-, 15-, or 20-year first phase holding period? (Use Schedule C, Form 4720, to determine
    if the foundation had excess business holdings in 2012.)....................
    3b
     
     
    4a
    Did the foundation invest during the year any amount in a manner that would jeopardize its charitable purposes?
    4a
     
    No
    b
    Did the foundation make any investment in a prior year (but after December 31, 1969) that could jeopardize its
    charitable purpose that had not been removed from jeopardy before the first day of the tax year beginning in 2012?
    4b
     
    No
    5a
    During the year did the foundation pay or incur any amount to:
    (1) Carry on propaganda, or otherwise attempt to influence legislation (section 4945(e))?
    (2) Influence the outcome of any specific public election (see section 4955); or to carry
    on, directly or indirectly, any voter registration drive?...............
    (3) Provide a grant to an individual for travel, study, or other similar purposes?
    (4) Provide a grant to an organization other than a charitable, etc., organization described
    in section 509(a)(1), (2), or (3), or section 4940(d)(2)? (see instructions)........
    (5) Provide for any purpose other than religious, charitable, scientific, literary, or
    educational purposes, or for the prevention of cruelty to children or animals?........
    b
    If any answer is “Yes” to 5a(1)–(5), did any of the transactions fail to qualify under the exceptions described in
    Regulations section 53.4945 or in a current notice regarding disaster assistance (see instructions)? ......
    5b
     
     
    .........bullet
    c
    If the answer is “Yes” to question 5a(4), does the foundation claim exemption from the
    tax because it maintained expenditure responsibility for the grant?............
    If “Yes,” attach the statement required by Regulations section 53.4945–5(d).
    6a
    Did the foundation, during the year, receive any funds, directly or indirectly, to pay premiums on
    a personal benefit contract?........................
    b
    Did the foundation, during the year, pay premiums, directly or indirectly, on a personal benefit contract?....
    6b
     
    No
    If “Yes” to 6b, file Form 8870.
    7a
    At any time during the tax year, was the foundation a party to a prohibited tax shelter transaction?
    b
    If yes, did the foundation receive any proceeds or have any net income attributable to the transaction? ....
    7b
     
    No
    Form 990-PF (2012)
    Form 990-PF (2012)
    Page 6
    Part VIII
    Information About Officers, Directors, Trustees, Foundation Managers, Highly Paid Employees,
    and Contractors
    1 List all officers, directors, trustees, foundation managers and their compensation (see instructions).
    (a) Name and address (b) Title, and average
    hours per week
    devoted to position     		(c) Compensation
     (If not paid, enter
    -0-)     		(d) Contributions to
    employee benefit plans
    and deferred compensation     		(e) Expense account,
    other allowances
    Nicolas Woodhouse PRESIDENT
    40.0     		203,092 0 0
    10 Memorial Blvd
    Providence,RI02903
    LANDON D CLAY TREASURER/DIRECTOR
    5.0     		0 0 0
    10 Memorial Blvd
    Providence,RI02903
    LAVINIA D CLAY SECRETARY/DIRECTOR
    5.0     		0 0 0
    10 Memorial Blvd
    Providence,RI02903
    Thomas M Clay Director
    5.0     		0 0 0
    10 Memorial Blvd
    Providence,RI02903
    Brian James CHIEF ADMIN OFFICER
    35.0     		80,000 3,935 0
    10 Memorial Blvd
    Providence,RI02903
    2 Compensation of five highest-paid employees (other than those included on line 1—see instructions). If none, enter “NONE.”
    (a) Name and address of each employee paid more than $50,000 (b) Title, and average
    hours per week
    devoted to position     		(c) Compensation (d) Contributions to
    employee benefit
    plans and deferred
    compensation     		(e) Expense account,
    other allowances
    JACK THORNE RESEARCH FELLOW
    40.0     		90,000 11,250 0
    10 MEMORIAL BLVD
    PROVIDENCE,RI02903
    SUCHARIT SARKAR RESEARCH FELLOW
    40.0     		82,500 12,295 0
    10 MEMORIAL BLVD
    PROVIDENCE,RI02903
    IVAN CORWIN RESEARCH FELLOW
    40.0     		82,500 4,132 0
    10 MEMORIAL BLVD
    PROVIDENCE,RI02903
    ROMAN TRAVKIN RESEARCH FELLOW
    40.0     		75,000 208 0
    10 MEMORIAL BLVD
    PROVIDENCE,RI02903
    Total number of other employees paid over $50,000...................bullet 0
    3 Five highest-paid independent contractors for professional services (see instructions). If none, enter "NONE".
    (a) Name and address of each person paid more than $50,000 (b) Type of service (c) Compensation
    Peter Scholze consulting services 95,980
    STEINWEG 32
    BONN   53121
    GM
    EAST HILL MGMT CO LLC MANAGEMENT SERVICES 190,110
    10 MEMORIAL BLVD SUITE 902
    PROVIDENCE,RI02903
    Total number of others receiving over $50,000 for professional services.............bullet0
    Part IX-A
    Summary of Direct Charitable Activities
    List the foundation’s four largest direct charitable activities during the tax year. Include relevant statistical information such as the number of organizations and other beneficiaries served, conferences convened, research papers produced, etc. Expenses
    1 CREATE NEW MATHEMATICAL KNOWLEDGE UTILIZING CMI PRIZE FELLOWS AND CMI SCHOLARS TO PERFORM CREATIVE MATHEMATICAL RESEARCH. 1,185,917
    2 DISSEMINATE MATHEMATICAL INSIGHT BY ORGANIZING WORKSHOPS, CONFERENCES, LECTURE SERIES, AND SUMMER SCHOOLS TO BRING MATHEMATICAL DEVELOPMENTS TO THE ATTENTION OF OTHERS. 284,673
    3 INSPIRE TALENTED STUDENTS IN PARTNERSHIP WITH OTHER INSTITUTIONS, RUN SUMMER PROGRAMS, AND ENCOURAGE OUTSTANDING STUDENTS TO PURSUE CAREERS IN MATHEMATICS. 221,837
    4  
    Form 990-PF (2012)
    Form 990-PF (2012)
    Page 7
    Part IX-B
    Summary of Program-Related Investments (see instructions)
    Describe the two largest program-related investments made by the foundation during the tax year on lines 1 and 2. Amount
    1  
    2  
    All other program-related investments. See page 24 of the instructions.
    3  
    Total. Add lines 1 through 3..........................bullet  
    Part X
    Minimum Investment Return (All domestic foundations must complete this part. Foreign foundations,
    see instructions.)
    1
    Fair market value of assets not used (or held for use) directly in carrying out charitable, etc.,
    purposes:
    a
    Average monthly fair market value of securities...................
    1a
    83,391,563
    b
    Average of monthly cash balances.......................
    1b
    385,892
    c
    Fair market value of all other assets (see instructions)................
    1c
    0
    d
    Total (add lines 1a, b, and c).........................
    1d
    83,777,455
    e
    Reduction claimed for blockage or other factors reported on lines 1a and
    1c (attach detailed explanation) .............
    1e
     
    2
    Acquisition indebtedness applicable to line 1 assets..................
    2
    0
    3
    Subtract line 2 from line 1d.........................
    3
    83,777,455
    4
    Cash deemed held for charitable activities. Enter 1 1⁄2% of line 3 (for greater amount, see
    instructions) .............................
    4
    1,256,662
    5
    Net value of noncharitable-use assets. Subtract line 4 from line 3. Enter here and on Part V, line 4
    5
    82,520,793
    6
    Minimum investment return. Enter 5% of line 5..................
    6
    4,126,040
    Part XI
    Distributable Amount bullet and do not complete this part.)
    1
    Minimum investment return from Part X, line 6....................
    1
     
    2a
    Tax on investment income for 2012 from Part VI, line 5......
    2a
     
    b
    Income tax for 2012. (This does not include the tax from Part VI.)...
    2b
     
    c
    Add lines 2a and 2b............................
    2c
     
    3
    Distributable amount before adjustments. Subtract line 2c from line 1............
    3
     
    4
    Recoveries of amounts treated as qualifying distributions................
    4
     
    5
    Add lines 3 and 4............................
    5
     
    6
    Deduction from distributable amount (see instructions).................
    6
     
    7
    Distributable amount as adjusted. Subtract line 6 from line 5. Enter here and on Part XIII,
    line 1................................
    7
     
    Part XII
    Qualifying Distributions (see instructions)
    1
    Amounts paid (including administrative expenses) to accomplish charitable, etc., purposes:
    a
    Expenses, contributions, gifts, etc.—total from Part I, column (d), line 26 ..........
    1a
    1,691,136
    b
    Program-related investments—total from Part IX-B..................
    1b
    0
    2
    Amounts paid to acquire assets used (or held for use) directly in carrying out charitable, etc.,
    purposes...............................
    2
    39,325
    3
    Amounts set aside for specific charitable projects that satisfy the:
    a
    Suitability test (prior IRS approval required)....................
    3a
    0
    b
    Cash distribution test (attach the required schedule) .................
    3b
    0
    4
    Qualifying distributions. Add lines 1a through 3b. Enter here and on Part V, line 8, and Part XIII, line 4
    4
    1,730,461
    5
    Foundations that qualify under section 4940(e) for the reduced rate of tax on net investment
    income. Enter 1% of Part I, line 27b (see instructions).................
    5
     
    6
    Adjusted qualifying distributions. Subtract line 5 from line 4..............
    6
    1,730,461
    Note: The amount on line 6 will be used in Part V, column (b), in subsequent years when calculating whether the foundation qualifies for
    the section 4940(e) reduction of tax in those years.
    Form 990-PF (2012)
    Form 990-PF (2012)
    Page 8
    Part XIII
    Undistributed Income (see instructions)
    (a)
    Corpus     		(b)
    Years prior to 2011     		(c)
    2011     		(d)
    2012
    1 Distributable amount for 2012 from Part XI, line 7 0
    2 Undistributed income, if any, as of the end of 2012:
    a Enter amount for 2011 only....... 0
    b Total for prior years:2010, 2009, 2008 0
    3 Excess distributions carryover, if any, to 2012:
    a From 2007....... 0
    b From 2008....... 0
    c From 2009....... 0
    d From 2010....... 0
    e From 2011....... 0
    fTotal of lines 3a through e......... 0
    4Qualifying distributions for 2012 from Part
    XII, line 4: bullet$ 1,730,461
    a Applied to 2011, but not more than line 2a 0
    b Applied to undistributed income of prior years
    (Election required—see instructions)......     		0
    c Treated as distributions out of corpus (Election
    required—see instructions).........     		 
    d Applied to 2012 distributable amount..... 0
    e Remaining amount distributed out of corpus 1,730,461
    5 Excess distributions carryover applied to 2012. 0 0
    (If an amount appears in column (d), the
    same amount must be shown in column (a).)
    6Enter the net total of each column as
    indicated below:
    a Corpus. Add lines 3f, 4c, and 4e. Subtract line 5 1,730,461
    b Prior years’ undistributed income. Subtract
    line 4b from line 2b ...........     		0
    c Enter the amount of prior years’ undistributed
    income for which a notice of deficiency has
    been issued, or on which the section 4942(a)
    tax has been previously assessed......     		 
    d Subtract line 6c from line 6b. Taxable amount
    —see instructions ...........     		0
    e Undistributed income for 2011. Subtract line
    4a from line 2a. Taxable amount—see
    instructions .............     		0
    f Undistributed income for 2012. Subtract
    lines 4d and 5 from line 1. This amount must
    be distributed in 2013 ..........     		0
    7 Amounts treated as distributions out of
    corpus to satisfy requirements imposed by
    section 170(b)(1)(F) or 4942(g)(3) (see
    instructions) .............     		 
    8Excess distributions carryover from 2007 not
    applied on line 5 or line 7 (see instructions) ...     		 
    9Excess distributions carryover to 2013.
    Subtract lines 7 and 8 from line 6a ......     		0
    10 Analysis of line 9:
    a Excess from 2008.... 0
    b Excess from 2009.... 0
    c Excess from 2010.... 0
    d Excess from 2011.... 0
    e Excess from 2012.... 0
    Form 990-PF (2012)
    Form 990-PF (2012)
    Page 9
    Part XIV
    Private Operating Foundations (see instructions and Part VII-A, question 9)
    1a If the foundation has received a ruling or determination letter that it is a private operating
    foundation, and the ruling is effective for 2012, enter the date of the ruling.......bullet
     
    b Check box to indicate whether the organization is a private operating foundation described in section or
    2a Enter the lesser of the adjusted net
    income from Part I or the minimum
    investment return from Part X for each
    year listed ..........     		Tax year Prior 3 years (e) Total
    (a) 2012 (b) 2011 (c) 2010 (d) 2009
    473,022 378,141 379,068 280,905 1,511,136
    b 85% of line 2a ......... 402,069 321,420 322,208 238,769 1,284,466
    c Qualifying distributions from Part XII,
    line 4 for each year listed .....     		1,730,461 2,777,771 2,502,167 3,474,244 10,484,643
    d Amounts included in line 2c not used directly
    for active conduct of exempt activities ....     		35,000 35,000 85,000 0 155,000
    e Qualifying distributions made directly
    for active conduct of exempt activities.
    Subtract line 2d from line 2c ....     		1,695,461 2,742,771 2,417,167 3,474,244 10,329,643
    3 Complete 3a, b, or c for the
    alternative test relied upon:
    a “Assets” alternative test—enter:
    (1) Value of all assets ...... 69,270,772 77,641,087 58,859,317 64,280,423 270,051,599
    (2) Value of assets qualifying
    under section 4942(j)(3)(B)(i)    		         0
    b “Endowment” alternative test— enter 2⁄3
    of minimum investment return shown in
    Part X, line 6 for each year listed...     		2,750,693 2,182,491 2,201,865 2,073,679 9,208,728
    c “Support” alternative test—enter:
    (1) Total support other than gross
    investment income (interest,
    dividends, rents, payments
    on securities loans (section
    512(a)(5)), or royalties) ....     		        0
    (2) Support from general public
    and 5 or more exempt
    organizations as provided in
    section 4942(j)(3)(B)(iii)....     		        0
    (3) Largest amount of support
    from an exempt organization    		         0
    (4) Gross investment income         0
    Part XV
    Supplementary Information (Complete this part only if the organization had $5,000 or more in
    assets at any time during the year—see instructions.)
    1Information Regarding Foundation Managers:
    aList any managers of the foundation who have contributed more than 2% of the total contributions received by the foundation
    before the close of any tax year (but only if they have contributed more than $5,000). (See section 507(d)(2).)
    LANDON T CLAY
    bList any managers of the foundation who own 10% or more of the stock of a corporation (or an equally large portion of the
    ownership of a partnership or other entity) of which the foundation has a 10% or greater interest.
    NONE
    2Information Regarding Contribution, Grant, Gift, Loan, Scholarship, etc., Programs:
    Check here bullet
    aThe name, address, and telephone number of the person to whom applications should be addressed:
    bThe form in which applications should be submitted and information and materials they should include:
    cAny submission deadlines:
    dAny restrictions or limitations on awards, such as by geographical areas, charitable fields, kinds of institutions, or other
    factors:
    Form 990-PF (2012)
    Form 990-PF (2012)
    Page 10
    Part XV
    Supplementary Information (continued)
    3 Grants and Contributions Paid During the Year or Approved for Future Payment
    Recipient If recipient is an individual,
    show any relationship to
    any foundation manager
    or substantial contributor
    		 Foundation
    status of
    recipient     		Purpose of grant or
    contribution     		Amount
    Name and address (home or business)
    aPaid during the year
    INDEPENDENT UNIVERSITY OF MOSCOW
    Bolshoy Vlasyevskiy Pereulok 11
    MOSCOW   119002
    RS     		NOT RELATED EXEMPT ORG EXEMPT PURPOSES 35,000
    Total .................................bullet 3a 35,000
    bApproved for future payment
    Total .................................bullet 3b  
    Form 990-PF (2012)
    Form 990-PF (2012)
    Page 11
    Part XVI-A
    Analysis of Income-Producing Activities
    Enter gross amounts unless otherwise indicated. Unrelated business income Excluded by section 512, 513, or 514 (e)
    Related or exempt
    function income
    (See instructions.)
    1Program service revenue: (a)
    Business code     		(b)
    Amount     		(c)
    Exclusion code     		(d)
    Amount
    a
    b
    c
    d
    e
    f
    gFees and contracts from government agencies          
    2 Membership dues and assessments....          
    3Interest on savings and temporary cash investments     14 12,438  
    4 Dividends and interest from securities....     14 455,816  
    5 Net rental income or (loss) from real estate:
    aDebt-financed property......          
    bNot debt-financed property.....          
    6Net rental income or (loss) from personal property          
    7 Other investment income.....          
    8Gain or (loss) from sales of assets other than inventory     18 8,783,226  
    9 Net income or (loss) from special events:          
    10 Gross profit or (loss) from sales of inventory..          
    11 Other revenue: aSALES OF BOOKS, VIDEOS & POSTERS         2,373
    bROYALTIES     15 2,395  
    c
    d
    e
    12 Subtotal. Add columns (b), (d), and (e)..   9,253,875 2,373
    13Total. Add line 12, columns (b), (d), and (e)..................
    139,256,248
    (See worksheet in line 13 instructions to verify calculations.)
    Part XVI-B
    Relationship of Activities to the Accomplishment of Exempt Purposes
    Line No.
    DownArrow     		Explain below how each activity for which income is reported in column (e) of Part XVI-A contributed importantly to
    the accomplishment of the foundation’s exempt purposes (other than by providing funds for such purposes). (See
    instructions.)
    Form 990-PF (2012)
    Form 990-PF (2012)
    Page 12
    Part XVII
    Information Regarding Transfers To and Transactions and Relationships With Noncharitable Exempt Organizations
    1
    Did the organization directly or indirectly engage in any of the following with any other organization described in section
    Yes
    No
    501(c) of the Code (other than section 501(c)(3) organizations) or in section 527, relating to political organizations?
    a
    Transfers from the reporting foundation to a noncharitable exempt organization of:
    (1) Cash...................................
    1a(1)
     
    No
    (2) Other assets.................................
    1a(2)
     
    No
    b
    Other transactions:
    (1) Sales of assets to a noncharitable exempt organization....................
    1b(1)
     
    No
    (2) Purchases of assets from a noncharitable exempt organization..................
    1b(2)
     
    No
    (3) Rental of facilities, equipment, or other assets.......................
    1b(3)
     
    No
    (4) Reimbursement arrangements...........................
    1b(4)
     
    No
    (5) Loans or loan guarantees.............................
    1b(5)
     
    No
    (6) Performance of services or membership or fundraising solicitations................
    1b(6)
     
    No
    c
    Sharing of facilities, equipment, mailing lists, other assets, or paid employees..............
    1c
     
    No
    d
    If the answer to any of the above is “Yes,” complete the following schedule. Column (b) should always show the fair market value
    of the goods, other assets, or services given by the reporting foundation. If the foundation received less than fair market value
    in any transaction or sharing arrangement, show in column (d) the value of the goods, other assets, or services received.
    (a) Line No. (b) Amount involved (c) Name of noncharitable exempt organization (d) Description of transfers, transactions, and sharing arrangements
    2a
    Is the foundation directly or indirectly affiliated with, or related to, one or more tax-exempt organizations
    described in section 501(c) of the Code (other than section 501(c)(3)) or in section 527?...........
    b
    If “Yes,” complete the following schedule.
    (a) Name of organization (b) Type of organization (c) Description of relationship
    Sign Here
    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 taxpayer or fiduciary) is based on all information of which preparer has any knowledge.
    Bullet Bullet
    May the IRS discuss this return
    with the preparer shown below
    (see instr.)?
    Signature of officer or trustee Date Title
    Paid Preparer Use Only Print/Type preparer's name Preparer's Signature Date PTIN
    Firm's namebullet



    Firm's addressbullet







         		Firm's EINbullet
    Phone no.
    Form 990-PF (2012)
    Additional Data


    Software ID:  
    Software Version:  


    Form 990PF - Special Condition Description:
    Special Condition Description

    TY 2012 AccountingFeesSchedule
    Name:
    THE CLAY MATHEMATICS INSTITUTE INC
    EIN: 13-4025978
    Category Amount Net Investment Income Adjusted Net Income Disbursements for Charitable Purposes
    WOLF & COMPANY 38,600 0 0 38,600
    Z&L ASSOCIATES 25,670 0 0 25,670

    Note: To capture the full content of this document, please select landscape mode (11" x 8.5") when printing.

    TY 2012 DepreciationSchedule
    Name:
    THE CLAY MATHEMATICS INSTITUTE INC
    EIN: 13-4025978
    Description of Property Date Acquired Cost or Other Basis Prior Years' Depreciation Computation Method Rate /
    Life (# of years)    		 Current Year's Depreciation Expense Net Investment Income Adjusted Net Income Cost of Goods Sold Not Included

    TY 2012 InvestmentsCorpStockSchedule
    Name:
    THE CLAY MATHEMATICS INSTITUTE INC
    EIN: 13-4025978
    Name of Stock End of Year Book Value End of Year Fair Market Value
    THROMBOGENICS NV 25,356,360 25,356,360
    BOEING CO. - DOMESTIC EQUITIES 11,750,000 11,750,000
    DOMESTIC EQUITIES 5,120,565 5,120,565
    DOMESTIC MUTUAL FUNDS 23,004 23,004
    EXXON MOBIL 3,613,680 3,613,680

    TY 2012 LandEtcSchedule2
    Name:
    THE CLAY MATHEMATICS INSTITUTE INC
    EIN: 13-4025978
    Category / Item Cost / Other Basis Accumulated Depreciation Book Value End of Year Fair Market Value


    TY 2012 LegalFeesSchedule
    Name:
    THE CLAY MATHEMATICS INSTITUTE INC
    EIN: 13-4025978
    Category Amount Net Investment Income Adjusted Net Income Disbursements for Charitable Purposes
    SULLIAN & WORCESTER LLP 27,275 0 0 27,275
    STEEL, DOEBLEY & GLASSMAN 15,304 0 0 15,304
    MASSBOW PARTNERS LLC 5,536 0 0 5,536


    TY 2012 OtherDecreasesSchedule
    Name:
    THE CLAY MATHEMATICS INSTITUTE INC
    EIN: 13-4025978
    Description Amount
    NET UNREALIZED GAINS/LOSSES 15,576,722


    TY 2012 OtherExpensesSchedule
    Name:
    THE CLAY MATHEMATICS INSTITUTE INC
    EIN: 13-4025978
    Description Revenue and Expenses per Books Net Investment Income Adjusted Net Income Disbursements for Charitable Purposes
    BANK SERVICE CHARGES 1,291 1,291 0 0
    ADVISORY BOARD 22,500 0 0 22,500
    INTERNET ACCESS FEES 3,624 0 0 3,624
    COMPUTER SUPPLIES & COSTS 925 0 0 925
    OFFICE SUPPPLIES 1,022 0 0 1,022
    ADVERTISING 3,933 0 0 3,933
    DUES AND SUBSCRIPTIONS 617 0 0 617
    UK ACCOUNTS SUPPORT 5,713 0 0 5,713
    PAYROLL PROCESSING FEES 3,185 0 0 3,185
    PARKING PERMITS 815 0 0 815
    SPEAKER HONORARIUM 40,826 0 0 40,826
    PHONE, POSTAGE & MAIL 4,859 0 0 4,859
    INSURANCE 16,609 0 0 16,609
    OTHER OFFICE EXPENSES 1,963 0 0 1,963
    UK CMI ADMINISTRATIVE MANAGER 25,637 0 0 25,637
    FORM 5500 PREPARATION 4,000 0 0 4,000


    TY 2012 OtherIncomeSchedule2
    Name:
    THE CLAY MATHEMATICS INSTITUTE INC
    EIN: 13-4025978
    Description Revenue And Expenses Per Books Net Investment Income Adjusted Net Income
    Royalties 2,395 0 2,395


    TY 2012 OtherLiabilitiesSchedule
    Name:
    THE CLAY MATHEMATICS INSTITUTE INC
    EIN: 13-4025978
    Description Beginning of Year - Book Value End of Year - Book Value
    SECURITY DEPOSIT 0 36,617


    TY 2012 OtherProfessionalFeesSchedule
    Name:
    THE CLAY MATHEMATICS INSTITUTE INC
    EIN: 13-4025978
    Category Amount Net Investment Income Adjusted Net Income Disbursements for Charitable Purposes
    OTHER CONSULTANT FEES 11,035 0 0 11,035
    EAST HILL MGMT - INV ADV FEE 190,110 190,110 0 0
    PETER SCHOLZE - CONSULTING FEE 95,980 0 0 95,980


    TY 2012 SalesOfInventoryList 
    Name:
    THE CLAY MATHEMATICS INSTITUTE INC
    EIN: 13-4025978

    Category Gross Sales Cost of Goods Sold Net (Gross Sales Minus
    Cost of Goods Sold)
    SALES OF BOOKS VIDEOS, POSTERS & MONITORS 2,373   2,373

    TY 2012 TaxesSchedule
    Name:
    THE CLAY MATHEMATICS INSTITUTE INC
    EIN: 13-4025978
    Category Amount Net Investment Income Adjusted Net Income Disbursements for Charitable Purposes
    PAYROLL TAXES 90,029 0 0 90,029
    FEDERAL TAXES 177,000 0 0 0