SECOND AMENDMENT TO UNSECURED CREDIT AGREEMENT

Exhibit 10.4

SECOND AMENDMENT TO UNSECURED CREDIT AGREEMENT

This Second Amendment to Unsecured Credit Agreement (the “Amendment”) is made as of August 2, 2012 (the “Effective Date”), by and among BIOMED REALTY, L.P., a Maryland limited partnership (“Borrower”), KEYBANK NATIONAL ASSOCIATION, as “Administrative Agent,” and such of the lenders (“Lenders”) party to the Loan Agreement (defined below) constituting the Requisite Lenders under the Loan Agreement, and, solely for the purpose of agreeing to the terms and conditions of Section 6 below, BIOMED REALTY TRUST, INC., a Maryland corporation (“Guarantor”).

R E C I T A L S

A. Borrower, Administrative Agent, the Lenders executing this Amendment and certain other Lenders have entered into that certain Unsecured Credit Agreement dated as of July 14, 2011, as amended by that certain First Amendment to Unsecured Credit Agreement dated as of March 30, 2012 (as it may be further amended, the “Loan Agreement”). All capitalized terms used herein and not otherwise defined shall have the meanings given to them in the Loan Agreement.

B. Borrower has requested that Administrative Agent and Lenders agree to amend the Loan Agreement as provided herein.

NOW, THEREFORE, with reference to the foregoing Recitals, all of which are incorporated herein by this reference, for valuable consideration, the receipt and sufficiency of which is hereby acknowledged, the parties hereto agree as follows:

AGREEMENTS

1. Amendments to Defined Terms. The following Definitions from Article 1 of the Loan Agreement are modified as follows:

A. The defined term “Project” is hereby deleted and replaced with the following:

“Project” means any parcel of real property located in (i) the 48 states that comprise the continental United States of America, or (ii) the District of Columbia, or (iii) the United Kingdom, or (iv) France, or (v) Germany, or (vi) Switzerland, which in each case is owned, leased or operated (in each case in whole or in part) by Borrower, or any of its Subsidiaries or Investment Affiliates and which is improved with a building or buildings primarily used or intended to be used for office, office/laboratory, research, warehouse or manufacturing purposes or other ancillary purposes such as a parking garage serving or in the vicinity of any such building.

B. The defined term “Total Unencumbered Asset Value” is hereby deleted and replaced with the following:

“Total Unencumbered Asset Value” means, as of any day, an amount equal to the sum of the following amounts for assets then owned or leased under a Mortgageable Ground Lease by a member of the Consolidated Group or an Investment Affiliate and valued as follows: (i) Adjusted NOI attributable to Unencumbered Projects that are wholly owned in fee simple (or wholly leased under a Mortgageable Ground Lease) by Borrower or a Wholly-Owned Subsidiary of Borrower divided by the Capitalization Rate (excluding, however, for purposes of this clause (i) and the following clauses (ii) and (iii) any such portion of such Adjusted NOI attributable to (a) Unencumbered Projects that were Unstabilized Projects at any time during the Fiscal Quarter with respect to which Adjusted NOI is determined, (b) Unencumbered Projects acquired after the first day of such Fiscal Quarter, or (c) Unencumbered Projects disposed of during or after such Fiscal Quarter); plus, without duplication (ii) the BioMed Pro Rata Share of Adjusted NOI attributable to Unencumbered Projects that are wholly owned in fee simple (or wholly leased under a Mortgageable Ground Lease, or a combination of owned in fee simple and leased under a Mortgageable Ground Lease) by a member of the Consolidated Group other than Borrower or a Wholly-Owned Subsidiary of Borrower, divided by the Capitalization Rate; plus (iii) the Consolidated Group Pro Rata Share of Adjusted NOI attributable to Unencumbered Projects that are wholly owned in fee simple (or wholly leased under a Mortgageable Ground Lease) by an Investment Affiliate, divided by the Capitalization Rate, provided that in the case of clauses (ii) and (iii), if the aggregate amount to be contributed to Total Unencumbered Asset Value on account of the Unencumbered Projects described therein would exceed ten percent (10%) of Total Unencumbered Asset Value, the excess of such aggregate contribution over such maximum percentage shall be excluded; plus (iv) with respect to Unencumbered Projects excluded from clauses (i), (ii) and (iii) because they are Unstabilized Projects, the greater of (a) the portion of such Adjusted NOI attributable to such Unstabilized Projects (or the BioMed Pro Rata Share or Consolidated Group Pro Rata Share, as the case may be, thereof with respect to any such Unstabilized Project owned by a member of the Consolidated Group other than Borrower or a Wholly-Owned Subsidiary of Borrower or owned by an Investment Affiliate), divided by the Capitalization Rate; and (b) the Consolidated Group’s GAAP cost basis (or the BioMed Pro Rata Share or Consolidated Group Pro Rata Share, as the case may be, thereof with respect to any such Unstabilized Project owned by a member of the Consolidated Group other than Borrower or a Wholly-Owned Subsidiary of Borrower or owned by Investment Affiliate) in such Unstabilized Project, provided that, in the case of clause (iv), if the amount to be contributed to Total Unencumbered Asset Value on account of the Unencumbered Projects described in such clause would exceed ten percent (10%) of Total Unencumbered Asset Value, the excess of such contribution over such maximum percentage shall be excluded; plus (v) the Consolidated Group’s GAAP cost basis (or the BioMed Pro Rata Share or Consolidated Group Pro Rata Share, as the case may be, thereof with respect to any such unencumbered land parcel owned by a member of the Consolidated Group other than Borrower or a Wholly-Owned Subsidiary of Borrower or by an Investment Affiliate) of all unencumbered land parcels, provided that, in the case of clause (v), if the amount to be contributed to Total Unencumbered Asset Value on account of the unencumbered land parcels described in such clause would exceed five percent (5%) of Total Unencumbered Asset Value, the excess of such contribution over such maximum percentage shall be excluded; plus (vi) the acquisition cost of all Unencumbered Projects acquired after the first day of the most recent Fiscal Quarter for which Adjusted NOI has been reported and on or prior to such date of determination (or the BioMed Pro Rata Share or Consolidated Group Pro Rata Share, as the case may be, of such acquisition cost with respect to any Unencumbered Project acquired by a member of the Consolidated Group other than Borrower or a Wholly-Owned Subsidiary of Borrower or by an Investment Affiliate),

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provided that with respect to each of the foregoing clauses of this sentence, if (X) the amount to be contributed to Total Unencumbered Asset Value on account of any single Unencumbered Project would exceed twenty percent (20%) of Total Unencumbered Asset Value, the excess of such contribution over such maximum percentage shall be excluded and (Y) the amount to be contributed to Total Unencumbered Asset Value on account of Foreign Projects would, in the aggregate, exceed fifteen percent (15%) of Total Unencumbered Asset Value, the excess of such contribution(s) over such maximum percentage shall be excluded. For purposes of determining Total Unencumbered Asset Value, Unencumbered Projects with negative Adjusted NOI, shall be excluded from clauses (i), (ii) or (iii) above.

C. The defined term “Unsecured Term Credit Agreement” is hereby deleted and replaced with the following:

“Unsecured Term Credit Agreement” means that certain Unsecured Credit Agreement dated as of March 30, 2012 by and among the Borrower, KeyBank and certain other lenders identified therein, as amended by that certain First Amendment to Unsecured Credit Agreement dated as of August 2, 2012, as it may be further amended or modified from time to time.

2. Additional Defined Terms. Article 1 of the Loan Agreement is hereby amended by the addition of the following new defined terms having the following meanings as provided herein:

A. “Dollar Equivalent” means on any date of determination, for the purposes of determining compliance with Article 5 or Article 6 or the existence of an Event of Default under Article 9 with respect to any amount denominated in a currency other than Dollars, the equivalent in Dollars of such amount, determined in good faith by the Borrower in a manner consistent with the way such amount is or would be reflected on the Borrower’s audited consolidated financial statements for the fiscal year in which such determination is made.

B. “Domestic Project” means any Project located in the 48 states that comprise the continental United States of America or in the District of Columbia.

C. “Foreign Project” means any Project located in (i) the United Kingdom, or (ii) France, or (iii) Germany, or (iv) Switzerland.

3. Amendments to Loan Agreement. The Loan Agreement is hereby amended as follows:

A. Dollar Equivalent. The following shall be added as new Section 1.6 to the Loan Agreement:

“1.6. Dollar Equivalent. Notwithstanding anything contained herein to the contrary, for purposes of any determination under Article 4, Article 5 or Article 6, all amounts incurred, outstanding or proposed to be incurred or outstanding in currencies other than Dollars shall be translated into the Dollar Equivalents of such amounts.”

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B. Interpretation of Terms. Section 11.2 of the Credit Agreement “[Intentionally Omitted]” is hereby deleted in its entirety and replaced with the following:

11.2. Interpretation of Terms. The parties to this Agreement agree that the following terms used herein shall have the correlative meanings ascribed to such terms or concepts in the United Kingdom:

(i) “leasehold mortgage”;

(ii) “fee simple”;

(iii) “fee owner”;

(iv) “first mortgage financing”;

(v) “Phase I report”; and

(vi) “Phase II report”.

4. Total Unencumbered Asset Value Calculation. As of the Effective Date, Schedule 3 to Exhibit B (Total Unencumbered Asset Value Calculation) to the Loan Agreement is hereby deleted in its entirety and replaced with the attached Schedule 3 to Exhibit B.

5. Schedule of Subsidiaries and Projects. As of the Effective Date, Schedule 4.4 (Subsidiaries) and Schedule 4.19 (Projects) to the Loan Agreement are hereby deleted in their entirety and replaced with the attached Schedule 4.4 and Schedule 4.19.

6. Guarantor. Guarantor (a) consents to the terms and conditions of this Amendment; and (b) reaffirms the Guaranty and confirms and agrees that, notwithstanding this Amendment and consummation of the transactions contemplated thereby, the Guaranty and all of such Guarantor’s covenants, obligations, agreements, waivers, and liabilities set forth in the Guaranty continue in full force and effect in accordance with their terms, modified only to the extent specifically set forth in this Amendment.

7. Full Force and Effect. Except as amended hereby, the terms and provisions of the Loan Agreement and the Loan Documents remain unchanged, are and shall remain in full force and effect unless and until modified or amended in writing in accordance with their terms, and are hereby ratified and confirmed. Except as expressly provided herein, this Amendment shall not constitute an amendment, waiver, consent or release with respect to any provision of any Loan Document, a waiver of any default or Event of Default under any Loan Document, or a waiver or release of any of the Lenders’ rights and remedies (all of which are hereby reserved). The Borrower expressly ratifies and confirms the confession of judgment (if applicable) and waiver of jury trial provisions contained in the Loan Documents.

8. References to Loan Documents; Capitalized Terms. Any and all references to any Loan Document in any other Loan Document shall be deemed to refer to such Loan Document as amended by this Amendment. This Amendment is deemed incorporated into each of the Loan Documents. Any initially capitalized terms used in this Amendment without definition shall have the meanings assigned to those terms in the Loan Documents. To the extent that any term or provision of this Amendment is or may be inconsistent with any term or provision in any Loan Document, the terms and provisions of this Amendment shall control.

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9. Successors and Assigns. This Amendment will be binding upon and inure to the benefit of the Borrower and the Lenders and their respective heirs, executors, administrators, successors and assigns.

10. Governing Law. This Amendment shall be governed by and construed in accordance with the laws of the State of New York.

11. Conditions to Effectiveness. This Amendment shall not be effective until each of the following conditions precedent have been fulfilled to the satisfaction of the Administrative Agent:

(a) The Administrative Agent shall have received counterparts of this Amendment duly executed and delivered by each of the parties hereto; and

(b) The Administrative Agent shall have received such certificates of resolutions or other action, incumbency certificates and/or other certificates of the Borrower, as Administrative Agent may require evidencing the identity, authority and capacity of each officer of the Borrower authorized to act in connection with this Amendment.

12. Representations and Warranties. The Borrower hereby represents and warrants to the Administrative Agent and the Lenders as of the date hereof that (i) the representations and warranties of Borrower, contained in Article 4 of the Loan Agreement (as amended by this Amendment) are true and correct in all material respects and (ii) no Event of Default or Default has occurred and is continuing.

13. Counterparts. This Amendment may be executed in any number of counterparts, all of which taken together shall constitute one agreement, and any of the parties hereto may execute this Amendment by signing any such counterpart.

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IN WITNESS WHEREOF, the parties have executed and delivered this Amendment as of the date first written above.

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SCHEDULE 3 TO EXHIBIT B

Contributions of Unencumbered Projects to Total Unencumbered Asset Value (All amounts previously multiplied by BioMed Pro Rata Share or Consolidated Group Pro Rata Share where applicable)

SCHEDULE 4.4

SUBSIDIARIES

SCHEDULE 4.19

PROJECTS