##### Table of Contents



UNITED STATES
SECURITIES AND EXCHANGE COMMISSION
 Washington, D.C. 20549
 
 Form 10-Q
 QUARTERLY REPORT
PURSUANT TO SECTION 13 OR 15(D)
OF THE SECURITIES EXCHANGE ACT OF 1934
 For the quarterly period ended March 31, 2009
 Commission File Number: 1-32261
 
 BIOMED REALTY TRUST, INC.
 (Exact name of registrant as specified in its charter)
 Maryland(State or other jurisdiction of 
incorporation or organization)
    
    20-1142292(I.R.S. Employer
Identification No.)17190 Bernardo Center Drive 
San Diego, California(Address of Principal Executive Offices)
    
    92128(Zip Code)
 (858) 485-9840  (Registrants telephone number, including area code)
 Yes þ No o
 Yes þ No o
  Large accelerated filer þ
    
    Accelerated filer o
    
    Non-accelerated filer o
    
    Smaller reporting company o(Do not check if a smaller reporting company)
 Yes o No þ




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##### 



BIOMED REALTY TRUST, INC.
 FORM 10-Q  QUARTERLY REPORT
FOR THE QUARTERLY PERIOD ENDED MARCH 31, 2009
TABLE OF CONTENTS
 PagePART I  FINANCIAL INFORMATIONItem 1 Consolidated Financial Statements
    
    
    3Consolidated Balance Sheets as of March 31, 2009 (Unaudited)
and December 31, 2008 (Unaudited)
    
    
    3Consolidated Statements of Income for the three months ended
March 31, 2009 and 2008 (Unaudited)
    
    
    4Consolidated Statements of Equity for the three months ended
March 31, 2009 and 2008 (Unaudited)
    
    
    5Consolidated Statements of Comprehensive Income/(Loss) for the
three months ended March 31, 2009 and 2008 (Unaudited)
    
    
    6Consolidated Statements of Cash Flows for the three months
ended March 31, 2009 and 2008 (Unaudited)
    
    
    7Notes to Consolidated Financial Statements (Unaudited)
    
    
    8Item 2 Managements Discussion and Analysis of Financial
Condition and Results of Operations
    
    
    27Item 3 Quantitative and Qualitative Disclosures About Market Risk
    
    
    35Item 4 Controls and Procedures
    
    
    36PART II  OTHER INFORMATIONItem 1 Legal Proceedings
    
    
    37Item 1A Risk Factors
    
    
    37Item 2 Unregistered Sales of Equity Securities and Use of Proceeds
    
    
    37Item 3 Defaults Upon Senior Securities
    
    
    37Item 4 Submission of Matters to a Vote of Security Holders
    
    
    37Item 5 Other Information
    
    
    37Item 6 Exhibits
    
    
    37SIGNATURES
    
    
    38Exhibit 10.1Exhibit 10.2Exhibit 31.1Exhibit 31.2Exhibit 32.1
   2




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##### Table of Contents



PART I  FINANCIAL INFORMATION
 
 ITEM 1. CONSOLIDATED FINANCIAL STATEMENTS
 BIOMED REALTY TRUST, INC.
 
 CONSOLIDATED BALANCE SHEETS
 (In thousands, except share data)
 (Unaudited)
 March 31, 2009
    
    
    December 31, 2008(Revised)ASSETSInvestments in real estate, net
    
    $
    3,001,077
    
    
    $
    2,960,429Investments in unconsolidated partnerships
    
    
    49,756
    
    
    
    18,173Cash and cash equivalents
    
    
    32,318
    
    
    
    21,422Restricted cash
    
    
    4,951
    
    
    
    7,877Accounts receivable, net
    
    
    14,749
    
    
    
    9,417Accrued straight-line rents, net
    
    
    62,040
    
    
    
    58,138Acquired above-market leases, net
    
    
    4,009
    
    
    
    4,329Deferred leasing costs, net
    
    
    95,204
    
    
    
    101,519Deferred loan costs, net
    
    
    8,451
    
    
    
    9,754Other assets
    
    
    37,607
    
    
    
    38,256Total assets
    
    $
    3,310,162
    
    
    $
    3,229,314LIABILITIES AND EQUITYMortgage notes payable, net
    
    $
    351,469
    
    
    $
    353,161Secured construction loan
    
    
    507,128
    
    
    
    507,128Secured term loan
    
    
    250,000
    
    
    
    250,000Exchangeable senior notes, net
    
    
    111,068
    
    
    
    122,043Unsecured line of credit
    
    
    204,334
    
    
    
    108,767Security deposits
    
    
    7,641
    
    
    
    7,623Dividends and distributions payable
    
    
    32,563
    
    
    
    32,445Accounts payable, accrued expenses, and other liabilities
    
    
    87,359
    
    
    
    66,821Derivative instruments
    
    
    100,840
    
    
    
    126,091Acquired below-market leases, net
    
    
    14,762
    
    
    
    17,286Total liabilities
    
    
    1,667,164
    
    
    
    1,591,365Equity:Stockholders equity:Preferred stock, $.01 par value, 15,000,000 shares
authorized: 7.375% Series A cumulative redeemable
preferred stock, $230,000,000 liquidation preference
($25.00 per share), 9,200,000 shares issued and
outstanding at March 31, 2009 and December 31, 2008
    
    
    222,413
    
    
    
    222,413Common stock, $.01 par value, 100,000,000 shares
authorized, 81,181,196 and 80,757,421 shares issued
and outstanding at March 31, 2009 and December 31,
2008, respectively
    
    
    812
    
    
    
    808Additional paid-in capital
    
    
    1,661,656
    
    
    
    1,661,009Accumulated other comprehensive loss
    
    
    (100,314
    )
    
    
    (112,126
    )Dividends in excess of earnings
    
    
    (154,708
    )
    
    
    (146,536
    )Total stockholders equity
    
    
    1,629,859
    
    
    
    1,625,568Noncontrolling interests
    
    
    13,139
    
    
    
    12,381Total equity
    
    
    1,642,998
    
    
    
    1,637,949Total liabilities and equity
    
    $
    3,310,162
    
    
    $
    3,229,314
   3




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##### Table of Contents



BIOMED REALTY TRUST, INC.
 
 CONSOLIDATED STATEMENTS OF INCOME
 (In thousands, except share data)
 (Unaudited)
 For the Three Months EndedMarch 31,2009
    
    
    2008(Revised)Revenues:Rental
    
    $
    68,419
    
    
    $
    50,342Tenant recoveries
    
    
    21,081
    
    
    
    16,582Other income
    
    
    4,451
    
    
    
    434Total revenues
    
    
    93,951
    
    
    
    67,358Expenses:Rental operations
    
    
    22,152
    
    
    
    13,865Real estate taxes
    
    
    7,233
    
    
    
    5,269Depreciation and amortization
    
    
    27,313
    
    
    
    17,687General and administrative
    
    
    5,280
    
    
    
    6,194Total expenses
    
    
    61,978
    
    
    
    43,015Income from operations
    
    
    31,973
    
    
    
    24,343Equity in net loss of unconsolidated partnerships
    
    
    (301
    )
    
    
    (172
    )Interest income
    
    
    63
    
    
    
    155Interest expense
    
    
    (12,080
    )
    
    
    (7,173
    )Loss on derivative instruments
    
    
    (56
    )
    
    
    Gain on extinguishment of debt
    
    
    4,371
    
    
    
    Net income
    
    
    23,970
    
    
    
    17,153Net income attributable to noncontrolling interests
    
    
    (705
    )
    
    
    (581
    )Preferred stock dividends
    
    
    (4,241
    )
    
    
    (4,241
    )Net income attributable to common stockholders
    
    $
    19,024
    
    
    $
    12,331Net income per share available to common stockholders:Basic and diluted earnings per share
    
    $
    0.23
    
    
    $
    0.19Weighted-average common shares outstanding:Basic
    
    
    80,261,363
    
    
    
    65,350,512Diluted
    
    
    84,499,365
    
    
    
    69,024,935
   4




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BIOMED REALTY TRUST, INC.
 
 CONSOLIDATED STATEMENTS OF EQUITY
 (In thousands, except share data)
 (Unaudited)
 AccumulatedSeries A
    
    
    
    
    
    
    
    
    
    
    Additional
    
    
    Other
    
    
    Dividends in
    
    
    TotalPreferred
    
    
    Common Stock
    
    
    Paid-In
    
    
    Comprehensive
    
    
    Excess of
    
    
    Stockholders
    
    
    Noncontrolling
    
    
    TotalStock
    
    
    Shares
    
    
    Amount
    
    
    Capital
    
    
    (Loss)/Income
    
    
    Earnings
    
    
    Equity
    
    
    Interests
    
    
    EquityBalance at December 31, 2008 (Revised)
    
    $
    222,413
    
    
    
    80,757,421
    
    
    $
    808
    
    
    $
    1,661,009
    
    
    $
    (112,126
    )
    
    $
    (146,536
    )
    
    $
    1,625,568
    
    
    $
    12,381
    
    
    $
    1,637,949Net issuances of unvested restricted common stock
    
    
    
    
    
    
    350,165
    
    
    
    3
    
    
    
    (34
    )
    
    
    
    
    
    
    
    
    
    
    (31
    )
    
    
    
    
    
    
    (31
    )Conversion of operating partnership units to common stock
    
    
    
    
    
    
    73,610
    
    
    
    1
    
    
    
    (153
    )
    
    
    
    
    
    
    
    
    
    
    (152
    )
    
    
    152
    
    
    
    Vesting of share-based awards
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    1,404
    
    
    
    
    
    
    
    
    
    
    
    1,404
    
    
    
    
    
    
    
    1,404Allocation of equity to noncontrolling interests
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    (570
    )
    
    
    
    
    
    
    
    
    
    
    (570
    )
    
    
    570
    
    
    
    Common stock dividends
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    (27,196
    )
    
    
    (27,196
    )
    
    
    
    
    
    
    (27,196
    )Net income
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    23,265
    
    
    
    23,265
    
    
    
    705
    
    
    
    23,970Preferred stock dividends
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    (4,241
    )
    
    
    (4,241
    )
    
    
    
    
    
    
    (4,241
    )OP unit distributions
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    (1,126
    )
    
    
    (1,126
    )Unrealized gain on marketable securities
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    549
    
    
    
    
    
    
    
    549
    
    
    
    21
    
    
    
    570Unrealized loss on derivative instruments
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    11,263
    
    
    
    
    
    
    
    11,263
    
    
    
    436
    
    
    
    11,699Balance at March 31, 2009
    
    $
    222,413
    
    
    
    81,181,196
    
    
    $
    812
    
    
    $
    1,661,656
    
    
    $
    (100,314
    )
    
    $
    (154,708
    )
    
    $
    1,629,859
    
    
    $
    13,139
    
    
    $
    1,642,998
   5




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BIOMED REALTY TRUST, INC.
 
 CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME/(LOSS)
 (In thousands)
 (Unaudited)
 Three Months EndedMarch 31,2009
    
    
    2008(Revised)Net income attributable to common stockholders and noncontrolling interests
    
    $
    19,729
    
    
    $
    12,912Other comprehensive income/(loss):Unrealized gain/(loss) on derivative instruments
    
    
    12,787
    
    
    
    (32,067
    )Equity in other comprehensive loss of unconsolidated partnerships
    
    
    (213
    )
    
    
    Deferred settlement payments derivative instruments, net
    
    
    (875
    )
    
    
    (995
    )Unrealized gain on marketable securities
    
    
    570
    
    
    
    Total other comprehensive income/(loss)
    
    
    12,269
    
    
    
    (33,062
    )Comprehensive income/(loss)
    
    
    31,998
    
    
    
    (20,150
    )Comprehensive (income)/loss attributable to noncontrolling interests
    
    
    (1,162
    )
    
    
    900Comprehensive income/(loss) attributable to common stockholders
    
    $
    30,836
    
    
    $
    (19,250
    )
   6




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##### Table of Contents



BIOMED REALTY TRUST, INC.
 
 CONSOLIDATED STATEMENTS OF CASH FLOWS
 (In thousands)
 (Unaudited)
 Three Months EndedMarch 31,2009
    
    
    2008(Revised)Operating activities:Net income
    
    $
    23,970
    
    
    $
    17,153Adjustments to reconcile net income to net cash provided by operating activities:Gain on extinguishment of debt
    
    
    (4,371
    )
    
    
    Loss on derivative instruments
    
    
    56
    
    
    
    Depreciation and amortization, including amounts for discontinued operations
    
    
    27,313
    
    
    
    17,687Allowance for doubtful accounts
    
    
    3,739
    
    
    
    91Revenue reduction attributable to acquired above-market leases
    
    
    320
    
    
    
    371Revenue recognized related to acquired below-market leases
    
    
    (3,902
    )
    
    
    (1,509
    )Revenue reduction attributable to lease incentives
    
    
    331
    
    
    
    126Compensation expense related to restricted common stock and LTIP units
    
    
    1,404
    
    
    
    1,382Amortization of deferred loan costs
    
    
    1,143
    
    
    
    563Amortization of debt premium on mortgage notes payable
    
    
    (455
    )
    
    
    (150
    )Amortization of debt discount on exchangeable senior notes
    
    
    483
    
    
    
    664Loss from unconsolidated partnerships
    
    
    301
    
    
    
    172Distributions representing return on capital from unconsolidated partnerships
    
    
    32
    
    
    
    19Changes in operating assets and liabilities:Restricted cash
    
    
    2,926
    
    
    
    516Accounts receivable
    
    
    (5,830
    )
    
    
    (350
    )Accrued straight-line rents
    
    
    (7,143
    )
    
    
    (4,267
    )Deferred leasing costs
    
    
    (2,909
    )
    
    
    (1,480
    )Other assets
    
    
    1,251
    
    
    
    2,110Security deposits
    
    
    18
    
    
    
    236Accounts payable, accrued expenses and other liabilities
    
    
    4,619
    
    
    
    (7,015
    )Net cash provided by operating activities
    
    
    43,296
    
    
    
    26,319Investing activities:Purchases of interests in and additions to investments in real estate and related intangible assets
    
    
    (45,367
    )
    
    
    (61,342
    )Distributions representing return of capital from unconsolidated partnerships
    
    
    
    
    
    
    1,373Contributions to unconsolidated partnerships, net of intercompany eliminations
    
    
    (32,131
    )
    
    
    (332
    )Receipts of master lease payments
    
    
    
    
    
    
    103Additions to non-real estate assets
    
    
    (125
    )
    
    
    (4,448
    )Net cash used in investing activities
    
    
    (77,623
    )
    
    
    (64,646
    )Financing activities:Payment of deferred loan costs
    
    
    (17
    )
    
    
    Unsecured line of credit proceeds
    
    
    95,567
    
    
    
    39,800Principal payments on mortgage notes payable
    
    
    (1,237
    )
    
    
    (1,446
    )Repurchases of exchangeable senior notes
    
    
    (6,910
    )
    
    
    Settlement of derivative instruments
    
    
    (8,860
    )
    
    
    Secured construction loan proceeds
    
    
    
    
    
    
    32,468Deferred settlement payments, net on interest rate swaps
    
    
    (875
    )
    
    
    (995
    )Distributions to operating partnership unit and LTIP unit holders
    
    
    (1,151
    )
    
    
    (1,029
    )Dividends paid to common stockholders
    
    
    (27,053
    )
    
    
    (20,326
    )Dividends paid to preferred stockholders
    
    
    (4,241
    )
    
    
    (4,241
    )Net cash provided by financing activities
    
    
    45,223
    
    
    
    44,231Net increase in cash and cash equivalents
    
    
    10,896
    
    
    
    5,904Cash and cash equivalents at beginning of period
    
    
    21,422
    
    
    
    13,479Cash and cash equivalents at end of period
    
    $
    32,318
    
    
    $
    19,383Supplemental disclosure of cash flow information:Cash paid during the period for interest (net of amounts capitalized of $4,130 and $15,064,
respectively)
    
    $
    10,821
    
    
    $
    9,186Supplemental disclosure of non-cash investing and financing activities:Accrual for preferred stock dividends declared
    
    $
    4,241
    
    
    $
    4,241Accrual for common stock dividends declared
    
    
    27,196
    
    
    
    21,974Accrual for distributions declared for operating partnership unit and LTIP unit holders
    
    
    1,126
    
    
    
    1,170Accrued additions to real estate and related intangible assets
    
    
    37,048
    
    
    
    54,037
   7




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##### Table of Contents



BIOMED REALTY TRUST, INC.
 
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
 (Unaudited)
 1. Organization and Description of Business
  2. Basis of Presentation and Summary of Significant Accounting Policies
  Principles of Consolidation
  Investments in Partnerships
 Consolidation of Variable Interest Entities Consolidated Financial Statements
  8




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##### Table of Contents



Determining Whether a General Partner, or the General Partners as a Group, Controls a Limited
Partnership or Similar Entity When the Limited Partners Have Certain Rights
   Investments in Real Estate
  March 31, 2009
    
    
    December 31, 2008(Revised)Land
    
    $
    365,154
    
    
    $
    347,878Land under development
    
    
    52,247
    
    
    
    69,529Buildings and improvements
    
    
    2,193,415
    
    
    
    2,104,072Construction in progress
    
    
    405,764
    
    
    
    439,221Tenant improvements
    
    
    164,700
    
    
    
    161,8393,181,280
    
    
    
    3,122,539Accumulated depreciation
    
    
    (180,203
    )
    
    
    (162,110
    )$
    3,001,077
    
    
    $
    2,960,429
  Impairment of Long-Lived Assets and Long-Lived Assets to be Disposed
   9




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##### Table of Contents



Deferred Leasing Costs
   Balance atMarch 31,
    
    
    Accumulated2009
    
    
    Amortization
    
    
    NetAcquired in-place leases
    
    $
    168,390
    
    
    $
    (99,770
    )
    
    $
    68,620Acquired management agreements
    
    
    12,921
    
    
    
    (9,444
    )
    
    
    3,477Deferred leasing and other direct costs
    
    
    29,226
    
    
    
    (6,119
    )
    
    
    23,107$
    210,537
    
    
    $
    (115,333
    )
    
    $
    95,204
  Balance atDecember 31,
    
    
    Accumulated2008
    
    
    Amortization
    
    
    NetAcquired in-place leases
    
    $
    168,390
    
    
    $
    (92,072
    )
    
    $
    76,318Acquired management agreements
    
    
    12,921
    
    
    
    (8,602
    )
    
    
    4,319Deferred leasing and other direct costs
    
    
    26,364
    
    
    
    (5,482
    )
    
    
    20,882$
    207,675
    
    
    $
    (106,156
    )
    
    $
    101,519
 Revenue Recognition
  
    
    whether the lease stipulates how and on what a tenant improvement allowance may be spent;
    
    whether the tenant or landlord retains legal title to the improvements;
    
    the uniqueness of the improvements;
    
    the expected economic life of the tenant improvements relative to the length of the
lease;
    
    the responsible party for construction cost overruns; and
    
    who constructs or directs the construction of the improvements.
   10




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##### Table of Contents



March 31,
    
    
    December 31,2009
    
    
    2008Acquired above-market leases
    
    $
    12,729
    
    
    $
    12,729Accumulated amortization
    
    
    (8,720
    )
    
    
    (8,400
    )$
    4,009
    
    
    $
    4,329
  March 31,
    
    
    December 31,2009
    
    
    2008Acquired below-market leases
    
    $
    39,339
    
    
    $
    37,961Accumulated amortization
    
    
    (24,577
    )
    
    
    (20,675
    )$
    14,762
    
    
    $
    17,286
  March 31,
    
    
    December 31,2009
    
    
    2008Lease incentives
    
    $
    11,718
    
    
    $
    11,698Accumulated amortization
    
    
    (2,542
    )
    
    
    (2,211
    )$
    9,176
    
    
    $
    9,487
 Reporting Revenue Gross as a Principal
versus Net as an Agent
    11




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##### Table of Contents



Investments
 Accounting for Certain Investments in Debt and Equity Securities Fair Value Measurements
 Share-Based Payments
 Share-Based Payment
 Assets and Liabilities Measured at Fair-Value
  The Fair Value Option for Financial
Assets and Financial Liabilities
    12




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##### Table of Contents



Derivative Instruments
 Disclosures about Derivative Instruments
and Hedging Activities, an amendment of FASB Statement No. 133 Accounting for Derivative Instruments and
Hedging Activities
     13




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Managements Estimates
  Segment Information
 Disclosures about Segments of an Enterprise and Related Information
 Reclassifications and Adoption of New Accounting Pronouncements
 Noncontrolling Interests in Consolidated Financial Statements Accounting for Convertible Debt Instruments That May Be
Settled in Cash Upon Conversion (Including Partial Cash Settlement) Accounting for Convertible Debt and Debt Issued with Stock Purchase Warrants Determining Whether Instruments Granted in
Share-Based Payment Transactions Are Participating Securities
  14




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##### Table of Contents



3. Equity
   Common Stock, Partnership Units and LTIP Units
  7.375% Series A Cumulative Redeemable Preferred Stock
  Dividends and Distributions
  Dividend and
    
    Dividend andAmount Per
    
    
    
    
    Distribution
    
    Distribution AmountDeclaration Date
    
    Securities Class
    
    Share/Unit
    
    
    Period Covered
    
    Payable Date
    
    (in thousands)March 16, 2009
    
    Common stock and
    
    $
    0.33500
    
    
    January 1, 2009 to
    
    April 15, 2009
    
    $
    28,322partnership and
    
    
    
    
    
    March 31, 2009LTIP unitsMarch 16, 2009
    
    Series A preferred
    
    $
    0.46094
    
    
    January 16, 2009 to
    
    April 15, 2009
    
    $
    4,241stock
    
    
    
    
    
    April 15, 2009
  15




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##### Table of Contents



Common stock, partnership units, and LTIP units
    
    $
    28,322Series A preferred stock
    
    
    4,241$
    32,563
 Noncontrolling Interests
 Classification and Measurement of Redeemable Securities
     March 31, 2009
    
    
    December 31, 2008Partnership Units
    
    
    Percentage of
    
    
    Partnership Units
    
    
    Percentage ofand LTIP Units
    
    
    Total
    
    
    and LTIP Units
    
    
    TotalBioMed Realty Trust
    
    
    80,340,929
    
    
    
    96.3
    %
    
    
    80,208,533
    
    
    
    96.3
    %Noncontrolling interest consisting of:Partnership and LTIP units held by
employees and related parties
    
    
    2,461,586
    
    
    
    2.9
    %
    
    
    2,961,369
    
    
    
    3.5
    %Partnership and LTIP units held by 

third parties(1)
    
    
    665,802
    
    
    
    0.8
    %
    
    
    122,192
    
    
    
    0.2
    %Total
    
    
    83,468,317
    
    
    
    100.0
    %
    
    
    83,292,094
    
    
    
    100.0
    %
 
 (1)
    
    Includes vested ownership interests held by a former employee which are now classified as
held by a third party.  16




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##### Table of Contents



4. Mortgage Notes Payable
  Stated Fixed
    
    
    Effective
    
    
    Principal BalanceInterest
    
    
    Interest
    
    
    March 31,
    
    
    December 31,Rate
    
    
    Rate
    
    
    2009
    
    
    2008
    
    
    Maturity DateArdentech Court
    
    
    7.25
    %
    
    
    5.06
    %
    
    $
    4,436
    
    
    $
    4,464
    
    
    July 1, 2012Bayshore Boulevard
    
    
    4.55
    %
    
    
    4.55
    %
    
    
    14,817
    
    
    
    14,923
    
    
    January 1, 2010Bridgeview Technology Park I
    
    
    8.07
    %
    
    
    5.04
    %
    
    
    11,347
    
    
    
    11,384
    
    
    January 1, 2011500 Kendall Street (Kendall D)
    
    
    6.38
    %
    
    
    5.45
    %
    
    
    67,386
    
    
    
    67,810
    
    
    December 1, 2018Lucent Drive
    
    
    5.50
    %
    
    
    5.50
    %
    
    
    5,289
    
    
    
    5,341
    
    
    January 21, 2015Monte Villa Parkway
    
    
    4.55
    %
    
    
    4.55
    %
    
    
    9,020
    
    
    
    9,084
    
    
    January 1, 20106828 Nancy Ridge Drive
    
    
    7.15
    %
    
    
    5.38
    %
    
    
    6,668
    
    
    
    6,694
    
    
    September 1, 2012Road to the Cure
    
    
    6.70
    %
    
    
    5.78
    %
    
    
    15,140
    
    
    
    15,200
    
    
    January 31, 2014Science Center Drive
    
    
    7.65
    %
    
    
    5.04
    %
    
    
    11,105
    
    
    
    11,148
    
    
    July 1, 2011Shady Grove Road
    
    
    5.97
    %
    
    
    5.97
    %
    
    
    147,000
    
    
    
    147,000
    
    
    September 1, 2016Sidney Street
    
    
    7.23
    %
    
    
    5.11
    %
    
    
    28,974
    
    
    
    29,184
    
    
    June 1, 20129885 Towne Centre Drive
    
    
    4.55
    %
    
    
    4.55
    %
    
    
    20,602
    
    
    
    20,749
    
    
    January 1, 2010900 Uniqema Boulevard
    
    
    8.61
    %
    
    
    5.61
    %
    
    
    1,317
    
    
    
    1,357
    
    
    May 1, 2015343,101
    
    
    
    344,338Unamortized premiums
    
    
    
    
    
    
    
    
    
    
    8,368
    
    
    
    8,823$
    351,469
    
    
    $
    353,161
   5. Credit Facilities, Exchangeable Senior Notes, and Other Debt Instruments
 Unsecured Line of Credit
   17




---



##### Table of Contents



Secured Term Loan
   Exchangeable Senior Notes, net
    18




---



##### Table of Contents



March 31,
    
    
    December 31,2009
    
    
    2008Exchangeable senior notes
    
    $
    116,250
    
    
    $
    128,250Unamortized debt discount(1)
    
    
    (5,182
    )
    
    
    (6,207
    )$
    111,068
    
    
    $
    122,043
 
 (1)
    
    The unamortized debt discount will be amortized through October 1, 2011, the first date at
which the holders of the Notes may require the Operating Partnership to repurchase the Notes.
Amortization of the debt discount during the three months ended March 31, 2009 and 2008
resulted in an effective interest rate of 6.5% on the Notes and additional interest expense of
approximately $483,000 and $662,000, respectively. Secured Construction Loan
   2009
    
    $
    510,9172010
    
    
    47,4462011
    
    
    230,5552012
    
    
    291,4212013
    
    
    4,862Thereafter(1)
    
    
    335,612$
    1,420,813
 
 (1)
    
    Includes $116.3 million in principal payments of the Notes based on a contractual maturity
date of October 1, 2026. 6. Earnings Per Share
 Determining Whether
Instruments Granted in Share-Based Payment Transactions Are Participating Securities
  19




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##### Table of Contents



Earnings
per Share
 Three Months EndedMarch 31,2009
    
    
    2008(Revised)Basic earnings per share:Net income attributable to common stockholders
    
    $
    19,024
    
    
    $
    12,331Less: net income allocable to unvested restricted stock
    
    
    (190
    )
    
    
    (49
    )Less: distributions in excess of earnings attributable to unvested restricted stock
    
    
    (93
    )
    
    
    (39
    )Net income available to common stockholders
    
    $
    18,741
    
    
    $
    12,243Diluted earnings per share:Net income attributable to common stockholders
    
    $
    19,024
    
    
    $
    12,331Plus: net income attributable to noncontrolling interests of operating partnership
    
    
    722
    
    
    
    589Net income available to common stockholders and participating securities (including
the Units)
    
    $
    19,746
    
    
    $
    12,920Weighted-average common shares outstanding:Basic
    
    
    80,261,363
    
    
    
    65,350,512Incremental shares from assumed conversion/vesting:Unvested restricted stock
    
    
    822,916
    
    
    
    235,458Operating partnership and LTIP units
    
    
    3,415,086
    
    
    
    3,438,965Diluted
    
    
    84,499,365
    
    
    
    69,024,935Basic and diluted earnings per share:Income per share  basic and diluted:Net income per share available to common stockholders
    
    $
    0.23
    
    
    $
    0.19
  20




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##### Table of Contents



7. Incentive Award Plan
     Weighted-Restricted Stock and
    
    
    Average Grant-LTIP Units
    
    
    Date Fair-ValueBalance at January 1, 2009
    
    
    900,841
    
    
    $
    18.92Granted
    
    
    353,600
    
    
    
    11.03Vested
    
    
    (179,658
    )
    
    
    27.04Balance at March 31, 2009
    
    
    1,074,783
    
    
    
    14.97
 Weighted-Restricted Stock and
    
    
    Average Grant-LTIP Units
    
    
    Date Fair-ValueBalance at January 1, 2008
    
    
    664,318
    
    
    $
    27.81Granted
    
    
    199,115
    
    
    
    22.29Vested
    
    
    (227,103
    )
    
    
    23.93Balance at March 31, 2008
    
    
    636,330
    
    
    
    26.37
  21




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##### Table of Contents



8. Investment in Unconsolidated Partnerships
  Companys
    
    
    CompanysOwnership
    
    
    EconomicName
    
    Partner
    
    Interest
    
    
    Interest
    
    
    Date AcquiredPREI I LLC(1)
    
    PREI
    
    
    20
    %
    
    
    20
    %
    
    April 4, 2007PREI II LLC(2)
    
    PREI
    
    
    20
    %
    
    
    20
    %
    
    April 4, 2007McKellar Court(3)
    
    Quidel Corporation
    
    
    21
    %
    
    
    21
    %(4)
    
    September 30, 2004
 
 (1)
    
    PREI I LLC acquired a portfolio of properties in Cambridge, Massachusetts comprised of a
stabilized laboratory/office building totaling 184,445 square feet located at 320 Bent Street,
a partially leased laboratory/office building totaling 420,000 square feet located at 301
Binney Street, a 37-unit apartment building, an operating garage facility on Rogers Street
with 503 spaces, an operating below grade garage facility at Kendall Square with approximately
1,400 spaces, and a building currently under construction at 650 East Kendall Street that the
Company believes can support up to 280,000 rentable square feet of laboratory and office
space. The 650 East Kendall Street site will also include a below grade parking facility that
the Company estimates can support up to 560 spaces upon completion.Each of the PREI operating agreements includes a put/call option whereby either member can cause
the limited liability company to sell certain properties in which it holds leasehold interests to
the Company at any time after the fifth anniversary and before the seventh anniversary of the
acquisition date. However, the put/call option may be terminated prior to exercise under certain
circumstances. The put/call option purchase price is based on a predetermined return on capital
invested by PREI. If the put/call option is exercised, the Company believes that it would have
adequate resources to fund the purchase price and also has the option to fund a portion of the
purchase price through the issuance of Company common stock.The PREI limited liability companies jointly entered into a secured acquisition and interim loan
facility with KeyBank and utilized approximately $427.0 million of that facility to fund a
portion of the purchase price for the properties acquired in April 2007. The remaining funds
available were utilized to fund construction costs at certain properties under development.
Pursuant to the loan facility, the Company executed guaranty agreements in which it guaranteed
the full completion of the construction and any tenant improvements at the 301 Binney Street
property if PREI I LLC is unable or unwilling to complete the project. On February 11, 2009, the
PREI joint ventures jointly refinanced the outstanding balance of the secured acquisition and
interim loan facility, or approximately $364.1 million, with the proceeds of a new loan totaling
$203.3 million and members capital contributions funding the balance due. The new loan bears
interest at a rate equal to, at the option of the PREI joint ventures, either (1) reserve
adjusted LIBOR plus 350 basis points or (2) the higher of (a) the prime rate then in effect, (b)
the federal funds rate then in effect plus 50 basis points or (c) one-month LIBOR plus 450 basis
points, and requires interest only monthly payments until the maturity date, February 10, 2011.
In addition, the PREI joint ventures may extend the maturity date of the secured acquisition and
interim loan facility to February 10, 2012 after satisfying certain conditions and paying an
extension fee based on the then current facility commitment. On March 11, 2009, the PREI joint
ventures jointly entered into an interest rate cap agreement, which is intended to have the
effect of hedging variability in future interest payments on the $203.3 million secured
acquisition and interim loan facility above a strike rate of 2.5% (excluding the applicable
credit spread) through February 10, 2011. At March 31, 2009, there were $203.3 million in
outstanding borrowings on the secured acquisition and interim loan facility, with a contractual
interest rate of 4.1% (including the applicable credit spread).(2)
    
    PREI II LLC acquired a portfolio of properties comprised of a development parcel in Houston,
Texas; a laboratory/office building totaling 259,706 rentable square feet and fee simple and
leasehold interests in surrounding land parcels located at the Science Park at Yale in New
Haven, Connecticut; and 25,000 rentable square feet of retail space and additional pad sites
for future development in Cambridge, Massachusetts. On August 2, 2007, PREI II LLC completed
the disposition of the 25,000 square feet of retail and additional pad sites in Cambridge,
Massachusetts. The total sale price included approximately $4.0 million contingently payable
in June 2012 pursuant to a put/call option, exercisable on the earlier of the extinguishment
or expiration of development restrictions placed on a portion of the development rights
included in the disposition. On September 28, 2007, PREI II LLC completed the disposition of
the laboratory/office building and the fee simple and leasehold interests in surrounding land
parcels in New Haven, Connecticut. On December 28, 2007, PREI II LLC completed the disposition
of the development parcel in Houston, Texas. None of the sales resulted in the recognition of
a material gain or loss. The Companys remaining investment in PREI II LLC (maximum exposure
to losses) was approximately $821,000 at March 31, 2009.(3)
    
    The McKellar Court partnership holds a property comprised of a two-story laboratory/office
building totaling 72,863 rentable square feet located in San Diego, California. The Companys
investment in the McKellar Court partnership (maximum exposure to losses) was approximately
$2.4 million at March 31, 2009.(4)
    
    The Companys economic interest in the McKellar partnership entitles it to 75% of the gains
upon a sale of the property and 21% of the operating cash flows.   22




---



##### Table of Contents



March 31,
    
    
    December 31,2009
    
    
    2008Assets:Investments in real estate, net
    
    $
    599,935
    
    
    $
    592,169Cash and cash equivalents (including restricted cash)
    
    
    6,322
    
    
    
    6,757Intangible assets, net
    
    
    14,527
    
    
    
    15,126Other assets
    
    
    19,484
    
    
    
    16,373Total assets
    
    $
    640,268
    
    
    $
    630,425Liabilities and equity:Mortgage notes payable
    
    $
    370,821
    
    
    $
    517,938Other liabilities
    
    
    24,080
    
    
    
    24,844Members equity
    
    
    245,367
    
    
    
    87,643Total liabilities and equity
    
    $
    640,268
    
    
    $
    630,425Companys net investment in unconsolidated partnerships
    
    $
    49,756
    
    
    $
    18,173
    Three Months EndedMarch 31,2009
    
    
    2008Total revenues
    
    $
    7,728
    
    
    $
    7,623Rental operations expense
    
    
    2,606
    
    
    
    1,834Real estate taxes
    
    
    2,121
    
    
    
    1,724Depreciation and amortization
    
    
    3,303
    
    
    
    2,248Interest expense, net of interest income
    
    
    2,089
    
    
    
    2,682Total expenses
    
    
    10,119
    
    
    
    8,488Net loss
    
    $
    (2,391
    )
    
    $
    (865
    )Companys equity in net loss of unconsolidated partnerships
    
    $
    (301
    )
    
    $
    (172
    )
 9. Derivatives and Other Financial Instruments
    23




---



##### Table of Contents



Fair-Value(1)Notional
    
    
    
    
    
    
    
    
    
    
    March 31,
    
    
    December 31,Amount
    
    
    Strike Rate
    
    
    Effective Date
    
    Expiration Date
    
    2009
    
    
    2008$
    250,000
    
    
    
    4.157
    %
    
    June 1, 2005
    
    June 1, 2010
    
    $
    (9,620
    )
    
    $
    (11,011
    )115,000
    
    
    
    4.673
    %
    
    October 1, 2007
    
    August 1, 2011
    
    
    (8,915
    )
    
    
    (9,349
    )35,000
    
    
    
    4.700
    %
    
    October 10, 2007
    
    August 1, 2011
    
    
    (2,741
    )
    
    
    (2,858
    )Interest rate swaps
    
    
    400,000
    
    
    
    
    
    
    
    
    
    
    
    (21,276
    )
    
    
    (23,218
    )150,000
    
    
    
    5.162
    %
    
    December 30, 2008
    
    December 30, 2018
    
    
    (29,856
    )
    
    
    (34,307
    )50,000
    
    
    
    5.167
    %
    
    December 30, 2008
    
    December 30, 2018
    
    
    
    
    
    
    (11,449
    )100,000
    
    
    
    5.167
    %
    
    December 30, 2008
    
    December 30, 2018
    
    
    (19,980
    )
    
    
    (22,942
    )150,000
    
    
    
    5.152
    %
    
    December 30, 2008
    
    December 30, 2018
    
    
    (29,728
    )
    
    
    (34,175
    )Forward starting swaps (2)
    
    $
    450,000
    
    
    
    
    
    
    
    
    
    
    $
    (79,564
    )
    
    $
    (102,873
    )Total derivative instruments
    
    $
    850,000
    
    
    
    
    
    
    
    
    
    
    $
    (100,840
    )
    
    $
    (126,091
    )
 
 (1)
    
    Fair-value of derivative instruments does not include any related accrued interest payable,
which is included in accrued expenses on the accompanying consolidated balance sheets.(2)
    
    One of the forward starting swaps was settled with the related counterparty in February 2009,
resulting in payment by the Company of approximately $8.9 million. As the forward starting
swap was no longer considered highly effective as of December 31, 2008, changes in the
fair-value of the derivative during the three months ended March 31, 2009 were recorded
directly in earnings in the consolidated statements of income. The other three forward
starting swaps, with notional values of $400.0 million, were settled subsequent to March 31,
2009 for approximately $77.6 million.    24




---



##### Table of Contents



Three Months EndedMarch 31,2009
    
    
    2008Amount of gain/(loss) recognized in other
comprehensive income (effective portion):Cash flow hedgesInterest rate swaps
    
    $
    1,987
    
    
    $
    (14,321
    )Forward starting swaps
    
    
    6,479
    
    
    
    (17,746
    )Total cash flow hedges
    
    
    8,466
    
    
    
    (32,067
    )Ineffective interest rate swaps
    
    
    4,321
    
    
    
    Total interest rate swaps
    
    $
    12,787
    
    
    $
    (32,067
    )
  Three Months EndedMarch 31,2009
    
    
    2008Amount of loss reclassified from other
comprehensive income to income (effective
portion):Cash flow hedgesInterest rate swaps
    
    $
    (3,905
    )
    
    $
    (797
    )Forward starting swaps
    
    
    
    
    
    
    Total cash flow hedges
    
    
    (3,905
    )
    
    
    (797
    )Ineffective interest rate swaps
    
    
    
    
    
    
    Total interest rate swaps
    
    $
    (3,905
    )
    
    $
    (797
    )
  Three Months EndedMarch 31,2009
    
    
    2008Amount of gain/(loss) recognized in income
(ineffective portion and amount excluded from
effectiveness testing):Cash flow hedgesInterest rate swaps
    
    $
    (9
    )
    
    $
    Forward starting swaps
    
    
    (352
    )
    
    
    Total cash flow hedges
    
    
    (361
    )
    
    
    Ineffective interest rate swaps
    
    
    305
    
    
    
    Total interest rate swaps
    
    $
    (56
    )
    
    $
    
  25




---



##### Table of Contents



10. New Accounting Standards
 Interim
Disclosures About Fair Value of Financial Instruments Disclosures about Fair Value of Financial Instruments Interim
Financial Reporting
 Recognition
and Presentation of Other-Than-Temporary Impairments
 Determining Fair Value When
the Volume and Level of Activity for the Asset or Liability Have Significantly Decreased and
Identifying Transactions That Are Not Orderly
   26




---



##### Table of Contents



ITEM 2. MANAGEMENTS DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS
    Overview
    27




---



##### Table of Contents



Consolidated Portfolio
    
    
    Unconsolidated Partnership Portfolio
    
    
    Total PortfolioPercent of
    
    
    
    
    
    
    
    
    
    
    Percent of
    
    
    
    
    
    
    
    
    
    
    Percent ofRentable
    
    
    Rentable
    
    
    
    
    
    
    Rentable
    
    
    Rentable
    
    
    
    
    
    
    Rentable
    
    
    RentableSquare
    
    
    Square
    
    
    
    
    
    
    Square
    
    
    Square
    
    
    
    
    
    
    Square
    
    
    SquareProperties
    
    
    Feet
    
    
    Feet Leased
    
    
    Properties
    
    
    Feet
    
    
    Feet Leased
    
    
    Properties
    
    
    Feet
    
    
    Feet LeasedStabilized properties
    
    
    41
    
    
    
    5,800,907
    
    
    
    98.6
    %
    
    
    4
    
    
    
    257,308
    
    
    
    100.0
    %
    
    
    45
    
    
    
    6,058,215
    
    
    
    98.7
    %Lease up properties
    
    
    17
    
    
    
    1,758,483
    
    
    
    55.9
    %
    
    
    2
    
    
    
    417,290
    
    
    
    27.3
    %
    
    
    19
    
    
    
    2,175,773
    
    
    
    50.5
    %Total operating portfolio
    
    
    58
    
    
    
    7,559,390
    
    
    
    88.7
    %
    
    
    6
    
    
    
    674,598
    
    
    
    55.1
    %
    
    
    64
    
    
    
    8,233,988
    
    
    
    85.9
    %Repositioning and redevelopment properties
    
    
    2
    
    
    
    1,543,858
    
    
    
    21.8
    %
    
    
    
    
    
    
    
    
    
    
    n/a
    
    
    
    2
    
    
    
    1,543,858
    
    
    
    21.8
    %Construction in progress
    
    
    2
    
    
    
    456,708
    
    
    
    68.5
    %
    
    
    1
    
    
    
    280,000
    
    
    
    
    
    
    
    3
    
    
    
    736,708
    
    
    
    42.5
    %Total portfolio
    
    
    62
    
    
    
    9,559,956
    
    
    
    76.9
    %
    
    
    7
    
    
    
    954,598
    
    
    
    38.9
    %
    
    
    69
    
    
    
    10,514,554
    
    
    
    73.5
    %Land parcels
    
    
    n/a
    
    
    
    1,352,000
    
    
    
    n/a
    
    
    
    
    
    
    
    
    
    
    
    n/a
    
    
    
    n/a
    
    
    
    1,352,000
    
    
    
    n/aTotal proforma portfolio(1)
    
    
    62
    
    
    
    10,911,956
    
    
    
    n/a
    
    
    
    7
    
    
    
    954,598
    
    
    
    n/a
    
    
    
    69
    
    
    
    11,866,554
    
    
    
    n/a
 
 (1)
    
    Percent of rentable square feet leased excludes undeveloped land parcels. Factors Which May Influence Future Operations
        28




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##### Table of Contents



Critical Accounting Policies
  New Accounting Standards
  Results of Operations
 Comparison of the Three Months Ended March 31, 2009 to the Three Months Ended March 31, 2008
  Redevelopment/DevelopmentSame Properties
    
    
    Properties
    
    
    New Properties
    
    
    Corporate2009
    
    
    2008
    
    
    2009
    
    
    2008
    
    
    2009
    
    
    2008
    
    
    2009
    
    
    2008Rental
    
    $
    54,311
    
    
    $
    49,217
    
    
    $
    13,965
    
    
    $
    1,025
    
    
    $
    147
    
    
    $
    104
    
    
    $
    (4
    )
    
    $
    (4
    )Tenant recoveries
    
    
    14,925
    
    
    
    16,090
    
    
    
    5,990
    
    
    
    336
    
    
    
    19
    
    
    
    5
    
    
    
    147
    
    
    
    151Other income
    
    
    3,904
    
    
    
    137
    
    
    
    5
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    542
    
    
    
    297Total revenues
    
    $
    73,140
    
    
    $
    65,444
    
    
    $
    19,960
    
    
    $
    1,361
    
    
    $
    166
    
    
    $
    109
    
    
    $
    685
    
    
    $
    444
 Rental Revenues.
 Tenant Recoveries.
  Other Income.
  29




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##### Table of Contents



Redevelopment/DevelopmentSame Properties
    
    
    Properties
    
    
    New Properties
    
    
    Corporate2009
    
    
    2008
    
    
    2009
    
    
    2008
    
    
    2009
    
    
    2008
    
    
    2009
    
    
    2008Rental operations
    
    $
    14,975
    
    
    $
    12,500
    
    
    $
    5,857
    
    
    $
    266
    
    
    $
    310
    
    
    $
    208
    
    
    $
    1,010
    
    
    $
    891Real estate taxes
    
    
    4,874
    
    
    
    5,030
    
    
    
    2,348
    
    
    
    230
    
    
    
    11
    
    
    
    9
    
    
    
    
    
    
    
    Depreciation and
amortization
    
    
    20,504
    
    
    
    17,218
    
    
    
    6,597
    
    
    
    427
    
    
    
    212
    
    
    
    42
    
    
    
    
    
    
    
    Total expenses
    
    $
    40,353
    
    
    $
    34,748
    
    
    $
    14,802
    
    
    $
    923
    
    
    $
    533
    
    
    $
    259
    
    
    $
    1,010
    
    
    $
    891
 Rental Operations Expense.
 Real Estate Tax Expense.
 Depreciation and Amortization Expense.
 General and Administrative Expenses.
 Equity in Net Loss of Unconsolidated Partnerships.
 Interest Expense.
   30




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##### Table of Contents



Loss on derivative instruments.
 Gain on Extinguishment of Debt.
 Noncontrolling Interests.
 Cash Flows
 Comparison of the Three Months Ended March 31, 2009 to the Three Months Ended March 31, 2008
 2009
    
    
    2008
    
    
    Change(In thousands)Net cash provided by operating activities
    
    $
    43,296
    
    
    $
    26,319
    
    
    $
    16,977Net cash used in investing activities
    
    
    (77,623
    )
    
    
    (64,646
    )
    
    
    (12,977
    )Net cash provided by financing activities
    
    
    45,223
    
    
    
    44,231
    
    
    
    992Ending cash and cash equivalents balance
    
    
    32,318
    
    
    
    19,383
    
    
    
    12,935
    Funds from Operations
   31




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##### Table of Contents



Three Months EndedMarch 31,2009
    
    
    2008(Revised)Net income attributable to common stockholders
    
    $
    19,024
    
    
    $
    12,331Adjustments:Noncontrolling interests in operating partnership
    
    
    722
    
    
    
    589Depreciation and amortization  unconsolidated partnerships
    
    
    662
    
    
    
    451Depreciation and amortization  consolidated entities
    
    
    27,313
    
    
    
    17,687Depreciation and amortization  allocable to
noncontrolling interest of consolidated joint ventures
    
    
    (20
    )
    
    
    (8
    )Funds from operations available to common shares and
Units
    
    $
    47,701
    
    
    $
    31,050Funds from operations per share  diluted
    
    $
    0.56
    
    
    $
    0.45Weighted-average common shares and Units outstanding  diluted
    
    
    84,499,365
    
    
    
    69,024,935
 Liquidity and Capital Resources
      32




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##### Table of Contents



Aggregate PrincipalAmount orShares/Units at
    
    
    Dollar Value
    
    
    Percent of TotalMarch 31, 2009
    
    
    Equivalent
    
    
    Capitalization(In thousands)Debt:Mortgage notes payable (1)
    
    
    
    
    
    $
    351,469
    
    
    
    15.7
    %Secured construction loan
    
    
    
    
    
    
    507,128
    
    
    
    22.8
    %Secured term loan
    
    
    
    
    
    
    250,000
    
    
    
    11.2
    %Exchangeable senior notes (2)
    
    
    
    
    
    
    111,068
    
    
    
    5.0
    %Unsecured line of credit
    
    
    
    
    
    
    204,334
    
    
    
    9.2
    %Total debt
    
    
    
    
    
    
    1,423,999
    
    
    
    63.9
    %Equity:Common shares outstanding (3)
    
    
    81,181,196
    
    
    
    549,597
    
    
    
    24.7
    %7.375% Series A Preferred shares outstanding (4)
    
    
    9,200,000
    
    
    
    230,000
    
    
    
    10.3
    %Operating partnership units outstanding (5)
    
    
    2,795,364
    
    
    
    18,925
    
    
    
    0.9
    %LTIP units outstanding (5)
    
    
    566,540
    
    
    
    3,835
    
    
    
    0.2
    %Total equity
    
    
    
    
    
    
    802,357
    
    
    
    36.1
    %Total capitalization
    
    
    
    
    
    $
    2,226,356
    
    
    
    100.0
    %
 
 (1)
    
    Amount includes debt premiums of $8.4 million recorded upon the assumption of the outstanding
indebtedness in connection with our purchase of the corresponding properties.(2)
    
    Amount includes a debt discount of $5.2 million recorded in accordance with FSP 14-1.(3)
    
    Based on the market closing price of our common stock of $6.77 per share on the last trading
day of the quarter (March 31, 2009).(4)
    
    Based on the liquidation preference of $25.00 per share for our 7.375% Series A preferred
stock.(5)
    
    Our partnership and LTIP units are each individually convertible into one share of common
stock using the market closing price of our common stock of $6.77 per share on the last
trading day of the quarter (March 31, 2009).   33




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##### Table of Contents



Off Balance Sheet Arrangements
      Principal Amount (1)Ownership
    
    
    
    
    
    
    March 31,
    
    
    December 31,Name
    
    Percentage
    
    
    Interest Rate (2)
    
    
    2009
    
    
    2008
    
    
    Maturity DatePREI I and PREI II(3)
    
    
    20
    %
    
    
    4.06
    %
    
    $
    40,650
    
    
    $
    72,811
    
    
    February 10, 2011PREI I(4)
    
    
    20
    %
    
    
    4.10
    %
    
    
    31,451
    
    
    
    28,706
    
    
    August 13, 2010McKellar Court(5)
    
    
    21
    %
    
    
    4.63
    %
    
    
    2,166
    
    
    
    2,175
    
    
    January 1, 2010Total
    
    
    
    
    
    
    
    
    
    $
    74,267
    
    
    $
    103,692
 
 (1)
    
    Amount represents our proportionate share of the total outstanding indebtedness for each of
the unconsolidated partnerships.(2)
    
    Effective or weighted average interest rate of the outstanding indebtedness as of March 31,
2009.(3)
    
    Amount represents our proportionate share of the total draws outstanding under a secured
acquisition and interim loan facility, which bears interest at a LIBOR-indexed variable-rate.
The secured acquisition and interim loan facility was utilized by both PREI I LLC and PREI II
LLC to acquire a portfolio of properties (initial borrowings of approximately $427.0 million)
on April 4, 2007 (see Note 8 in the accompanying consolidated financial statements). On
February 11, 2009, our PREI joint ventures jointly refinanced the outstanding balance of the
secured acquisition and interim loan facility, or approximately $364.1 million, with the
proceeds of a new loan totaling $203.3 million and members capital contributions funding the
balance due. The new loan bears interest at a rate equal to, at the option of our PREI joint
ventures, either (1) reserve adjusted LIBOR plus 350 basis points or (2) the higher of (a) the
prime rate then in effect, (b) the federal funds rate then in effect plus 50 basis points or
(c) one-month LIBOR plus 450 basis points, and requires interest only monthly payments until
the maturity date, February 10, 2011.(4)
    
    Amount represents our proportionate share of a secured construction loan, which bears
interest at a LIBOR-indexed variable-rate. The secured construction loan was executed by a
wholly owned subsidiary of PREI I LLC in connection with the construction of the 650 East
Kendall Street property (initial borrowings of $84.0 million on February 13, 2008 were used in
part to repay a portion of the secured acquisition and interim loan facility). The remaining
balance is being utilized to fund construction costs at the property.(5)
    
    Amount represents our proportionate share of the principal balance outstanding on a mortgage
note payable, which is secured by the McKellar Court property (excluding $86,000 of
unamortized debt premium).  34




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##### Table of Contents



Cash Distribution Policy
 i.e.
  Dividend
    
    
    DividendQuarter Ended
    
    Date Declared
    
    Date Paid
    
    per Common Share
    
    
    per Preferred ShareMarch 31, 2007
    
    March 15, 2007
    
    April 16, 2007
    
    $
    0.3100
    
    
    $
    0.45582June 30, 2007
    
    June 15, 2007
    
    July 16, 2007
    
    
    0.3100
    
    
    
    0.45582September 30, 2007
    
    September 14, 2007
    
    October 15, 2007
    
    
    0.3100
    
    
    
    0.46094December 31, 2007
    
    December 12, 2007
    
    January 15, 2008
    
    
    0.3100
    
    
    
    0.46094March 31, 2008
    
    March 14, 2008
    
    April 15, 2008
    
    
    0.3350
    
    
    
    0.46094June 30, 2008
    
    June 16, 2008
    
    July 15, 2008
    
    
    0.3350
    
    
    
    0.46094September 30, 2008
    
    September 15, 2008
    
    October 15, 2008
    
    
    0.3350
    
    
    
    0.46094December 31, 2008
    
    December 15, 2008
    
    January 15, 2009
    
    
    0.3350
    
    
    
    0.46094March 31, 2009
    
    March 16, 2009
    
    April 15, 2009
    
    
    0.3350
    
    
    
    0.46094
 Inflation
   
 ITEM 3. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK
   Effective InterestPercent of
    
    
    Rate atPrincipal Balance (1)
    
    
    Total Debt
    
    
    March 31, 2009Fixed interest rate (2)
    
    $
    462,537
    
    
    
    32.5
    %
    
    
    5.75
    %Variable interest rate (3)
    
    
    961,462
    
    
    
    67.5
    %
    
    
    3.69
    %Total/effective interest rate
    
    $
    1,423,999
    
    
    
    100.0
    %
    
    
    4.33
    %
 
 (1)
    
    Principal balance includes only consolidated indebtedness.  35




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##### Table of Contents



(2)
    
    Includes 13 mortgage notes payable secured by certain of our properties (including $8.4
million of unamortized premium) and our exchangeable senior notes (including $5.2 million of
unamortized debt discount).(3)
    
    Includes our unsecured line of credit, secured term loan, and secured construction loan,
which bear interest based on a LIBOR-indexed variable interest rate, plus a credit spread.
However, we are party to two interest rate swaps, which were intended to have the effect of
initially fixing the interest rates on $150.0 million of our variable-rate borrowings at 5.9% (based on the applicable
credit spreads for the underlying debt). We have also entered into an interest rate swap
agreement that is intended to fix the interest rate on the entire $250.0 million outstanding
balance of the secured term loan at a rate of 5.8% (including the credit spread for the $250.0
million secure term loan) until the interest rate swap expires in 2010. We have also entered into
two forward starting swap agreements designated as cash flow hedges, which will have the effect
of fixing the interest rate on $300.0 million of forecasted debt issuance (after retirement of
the secured construction loan) at approximately 5.2%.    
 ITEM 4. CONTROLS AND PROCEDURES
     36




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##### Table of Contents



PART II  OTHER INFORMATION
 
 ITEM 1. LEGAL PROCEEDINGS
  
 ITEM 1A. RISK FACTORS
  
 ITEM 2. UNREGISTERED SALES OF EQUITY SECURITIES AND USE OF PROCEEDS
  
 ITEM 3. DEFAULTS UPON SENIOR SECURITIES
  
 ITEM 4. SUBMISSION OF MATTERS TO A VOTE OF SECURITY HOLDERS
  
 ITEM 5. OTHER INFORMATION
  
 ITEM 6. EXHIBITS
 ExhibitNumber
    
    Description of Exhibit10.1
    
    
    Final 415 Regulations Amendment to the BioMed Realty 401(k) Retirement Savings Plan.10.2
    
    
    Sixth Amendment to the BioMed Realty 401(k) Retirement Savings Plan.31.1
    
    
    Certification of Chief Executive Officer pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.31.2
    
    
    Certification of Chief Financial Officer pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.32.1
    
    
    Certifications of Chief Executive Officer and Chief Financial Officer pursuant to 18 U.S.C.
Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.
  37




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##### Table of Contents



SIGNATURES
  BioMed Realty Trust, Inc./s/ ALAN D. GOLDAlan D. GoldChairman of the Board and Chief Executive Officer
(Principal Executive Officer)/s/ KENT GRIFFINKent GriffinPresident, Chief Operating Officer and Chief Financial Officer
(Principal Financial Officer)   38




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##### Table of Contents



ExhibitNumber
    
    Description of Exhibit10.1
    
    
    Final 415 Regulations Amendment to the BioMed Realty 401(k) Retirement Savings Plan.10.2
    
    
    Sixth Amendment to the BioMed Realty 401(k) Retirement Savings Plan.31.1
    
    
    Certification of Chief Executive Officer pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.31.2
    
    
    Certification of Chief Financial Officer pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.32.1
    
    
    Certifications of Chief Executive Officer and Chief Financial Officer pursuant to 18 U.S.C.
Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.
  39