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        <Explanation>The Whitehead Institute for Biomedical Research's (the "Institute") art collection was purchased with a gift from its founder, Edwin Whitehead. The collection consists of 77 artworks executed in oil, acrylic, watercolor and mixed media, prints and photography. The collection's purpose is to help create/foster a stimulating environment that promotes an innovative culture to achieve the mission of the Institute. Endowment Schedule D, Part V, Line 4 The Institute's endowment funds are used to underwrite the research program of the Institute as well as to fund the administration and operation of the Institute. FIN 48 Schedule D, Part X The institute is exempt from federal income tax under Section 501(c)(3) of the U.S. Internal Revenue Code. The institute complies with Financial Accounting Standards Board (FASB) Interpretation No. 38, Accounting for Uncertainty in Income Taxes - an Interpretation of FASB Statement 109 (FIN 48). Schedule D, Part XI, Line 8 Postretirement - 610,348 Grant Recovery - (527,064) Total - 83,284 Schedule D, Part XII, Line 2d Broad Rental Expenses - 4,948,787 Schedule D, Part XIII, Line 2d Broad Rental Expenses - 4,948,787</Explanation>
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      <PubViaBroadcastMediaExpln>NOTICE OF THE NON-DISCRIMINATORY POLICY IS PUBLISHED ANNUALLY IN THE SUNDAY EDUCATION SECTION OF THE BOSTON GLOBE. ALSO, ALL JOB POSTINGS LISTED ON WHITEHEAD INSTITUTES' EXTERNAL WEBSITE STATES THAT THE INSTITUTE IS AN EQUAL OPPORTUNITY EMPLOYER.</PubViaBroadcastMediaExpln>
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      <Form990ScheduleJPartII>
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        <BonusFilingOrg>0</BonusFilingOrg>
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      <Form990ScheduleJPartIII>
        <Identifier>schedule J, Part 1a and 1b</Identifier>
        <ReturnReference>David Page receives a housing allowance. No written policy is currently in</ReturnReference>
        <Explanation>place, however the board approved housing allowance as part of the compensation package for Directors of the Institute. Schedule J, Part 1, Line 4b: Martin Mullins: $16,500 457(b) Plan; Rudolf Jaenisch: $16,500 457(b) Plan; and John Travia: $16,500 457(b) Plan</Explanation>
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        </IssuerName>
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        <IssuePrice>7000000</IssuePrice>
        <DescriptionOfPurpose>EQUIPMENT PURCHASES</DescriptionOfPurpose>
        <Defeased>false</Defeased>
        <OnBehalfOfIssuer>false</OnBehalfOfIssuer>
      </Form990ScheduleKPartI>
      <Form990ScheduleKPartI>
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        </IssuerName>
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        <DateIssued>2008-10-30</DateIssued>
        <IssuePrice>4000000</IssuePrice>
        <DescriptionOfPurpose>EQUIPMENT PURCHASES</DescriptionOfPurpose>
        <Defeased>false</Defeased>
        <OnBehalfOfIssuer>false</OnBehalfOfIssuer>
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        <CapitalExpenditures>7411220</CapitalExpenditures>
        <YearOfSubstCompletion>2009</YearOfSubstCompletion>
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        <AdvanceRefunding>false</AdvanceRefunding>
        <FinalAllocationMade>true</FinalAllocationMade>
        <AdequateBooksAndRecdsMaintaind>true</AdequateBooksAndRecdsMaintaind>
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        <NamePerson>HIDDE PLOEGH -</NamePerson>
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        <LoanFromOrganization>X</LoanFromOrganization>
        <OriginalPrincipalAmount>350000</OriginalPrincipalAmount>
        <BalanceDue>231250</BalanceDue>
        <Default>false</Default>
        <ApprovedByBoard>true</ApprovedByBoard>
        <WrittenAgreement>true</WrittenAgreement>
      </LoanTable>
      <LoanTable>
        <NamePerson>DAVID PAGE -</NamePerson>
        <PurposeOfLoan>MORTGAGE ASSISTANCE</PurposeOfLoan>
        <LoanFromOrganization>X</LoanFromOrganization>
        <OriginalPrincipalAmount>350000</OriginalPrincipalAmount>
        <BalanceDue>302421</BalanceDue>
        <Default>false</Default>
        <ApprovedByBoard>true</ApprovedByBoard>
        <WrittenAgreement>true</WrittenAgreement>
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        <NameOfInterestedPerson>
          <NamePerson>MERCK CO INC</NamePerson>
        </NameOfInterestedPerson>
        <Relationship>TRUSTEE AS OFFICER</Relationship>
        <AmountOfTransaction>259754</AmountOfTransaction>
        <DescriptionOfTransaction>ROYALTY PAYMENTS ON PATENTS</DescriptionOfTransaction>
        <SharingOfRevenues>false</SharingOfRevenues>
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    </IRS990ScheduleL>
    <IRS990ScheduleM documentId="IRS990ScheduleM">
      <WorksOfArt />
      <ArtHistoricalTreasures />
      <ArtFractionalInterest />
      <BooksAndPublications />
      <ClothingAndHouseholdGoods />
      <CarsAndOtherVehicles />
      <BoatsAndPlanes />
      <IntellectualProperty />
      <SecuritiesPubliclyTraded>
        <NonCashCheckbox>X</NonCashCheckbox>
        <NumberOfContributions>8</NumberOfContributions>
        <NoncashContribsRptdF990>123081</NoncashContribsRptdF990>
        <MethodOfDeterminingRevenues>AVG OF HI/LOW</MethodOfDeterminingRevenues>
      </SecuritiesPubliclyTraded>
      <SecuritiesCloselyHeldStock />
      <SecuritiesPrtnrshpTrustIntrsts />
      <SecuritiesMiscellaneous />
      <QualifiedContribHistStruct />
      <QualifiedContribOther />
      <RealEstateResidential />
      <RealEstateCommercial />
      <RealEstateOther />
      <Collectibles />
      <FoodInventory />
      <DrugsAndMedicalSupplies />
      <Taxidermy />
      <HistoricalArtifacts />
      <ScientificSpecimens />
      <ArchaeologicalArtifacts />
      <NumberOf8283Received>0</NumberOf8283Received>
      <AnyPropertyThatMustBeHeld>false</AnyPropertyThatMustBeHeld>
      <ReviewProcessUnusualNCGifts>true</ReviewProcessUnusualNCGifts>
      <ThirdPartiesUsed>true</ThirdPartiesUsed>
      <Form990ScheduleMPartII>
        <Identifier>Schedule M, Column B</Identifier>
        <ReturnReference>The organization is reporting the number of contributions.</ReturnReference>
        <Explanation>Schedule M, Line 32 Gifts of stock are sent directly to UBS for immediate sale.</Explanation>
      </Form990ScheduleMPartII>
    </IRS990ScheduleM>
    <IRS990ScheduleO documentId="IRS990ScheduleO">
      <GeneralExplanation>
        <Identifier>MISSION</Identifier>
        <ReturnReference>FORM 990, PART I, LINE 1 AND PART III, LINE 1</ReturnReference>
        <Explanation>The Whitehead Institute for Biomedical Research (the "Institute") engages in biomedical research and education to foster the understanding of biological systems, organisms, and processes with the ultimate goal of improving human health and well-being. Volunteers Form 990, Part I, Line 6 The Institute does not formally track volunteers but has included the number of board members and committee members of the board of associates (friends of the institute) that are uncompensated. FORM 990, PART V, LINE 4 The Institute filed Form TD F 90-22.1 with respect to investments in certain Cayman Islands entities for Calendar Year 2009. The Institute is re-evaluating whether it is required to file Form TD F 90-22.1 for these investments for calendar year 2010 in light of the recently released treasury regulations.</Explanation>
      </GeneralExplanation>
      <GeneralExplanation>
        <Identifier>RELATIONSHIPS</Identifier>
        <ReturnReference>FORM 990, PART VI, LINE 2</ReturnReference>
        <Explanation>JOHN, PETER, AND SUSAN WHITEHEAD (ALL DIRECTORS) have a family relationship. Form 990, Part VI, Line 7A At least three members of the Institute's Board must be selected from candidates designated by Massachusetts Institute of Technology, ("MIT"). Form 990, Part VI, Line 11 The process for the FY2010 Form 990 includes review by senior management, the audit committee, and the independent external tax consultants. The audit committee reviews a draft of the return and the full board receives a final copy of the Form 990 before it is filed. CONFLICT OF INTEREST POLICY FORM 990, PART VI, LINE 12 Promptly after the end of each fiscal year of the Institute (June 30), and immediately following election to the Board for the first time, directors and officers shall submit to the Vice President, or such person as the Director may designate, a completed Disclosure Statement reporting information specifically requested in the Statement and also reporting on behalf of themselves, their family members, and organizations with which they have a business relationship, any actual or planned business or other transaction or relationship that directly or indirectly involves the Institute or that for some other reason could be construed as a conflict of interest because it might affect their independent, unbaised judgement when carrying out their duties for the Institute. If a matter comes before the Board or any committee of the Board, in which a director has an interest (either directly or indirectly), such director should withdraw from discussion and voting when the Board or committee acts on such matter. Conflicts of interest are monitored by the vice President and Director who advises the chairman of the board. Compensation Determination FORM 990, Part VI, Line 15 There is a Compensation Committee of the Board of Directors that annually reviews and recommends changes of the President's salary. The last review was conducted in fiscal year 2010. Faculty salaries are set by MIT yearly. All other officer salaries are part of a raise pool that is determined annually and approved by the Board of Directors as part of the budget approval process. AVAILABILITY OF DOCUMENTS FORM 990, PART VI, LINE 19 The institute's governing documents, conflict of interest policy, and financial statements are available on request.</Explanation>
      </GeneralExplanation>
    </IRS990ScheduleO>
  </ReturnData>
</Return>