##### 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 September 30, 2006.
  Commission File Number: 1-32261
      
 BIOMED REALTY TRUST,
    INC.
 (Exact name of registrant as
    specified in its charter)
  Maryland

20-1142292(State or other jurisdiction
    of
    incorporation or organization)

(I.R.S. Employer
    Identification No.)17140 Bernardo Center Drive,
    Suite 222
    San Diego, California

92128(Zip Code)(Address of Principal Executive
    Offices)   (858) 485-9840
 (Registrants telephone
    number, including area code)
    þ o
  Rule 12b-2
 þ o o
  Rule 12b-2 o þ




---



##### 



BIOMED
    REALTY TRUST, INC.
  FORM 10-Q 
    QUARTERLY REPORT
    FOR THE QUARTERLY PERIOD ENDED SEPTEMBER 30, 2006
  TABLE OF
    CONTENTS
  PagePART I 
    FINANCIAL INFORMATIONItem 1


Consolidated
    Financial StatementsConsolidated
    Balance Sheets for BioMed Realty Trust, Inc. as of
    September 30, 2006 (Unaudited) and December 31,
    2005


3Consolidated
    Statements of Income for BioMed Realty Trust, Inc. for the three
    and nine months ended September 30, 2006 and 2005
    (Unaudited)


4Consolidated
    Statements of Cash Flows for BioMed Realty Trust, Inc. for the
    nine months ended September 30, 2006 and 2005
    (Unaudited)


5Notes to
    Consolidated Financial Statements (Unaudited)


6Item 2


Managements
    Discussion and Analysis of Financial Condition and Results of
    Operations


21Item 3


Quantitative and
    Qualitative Disclosures About Market Risk


29Item 4


Controls and
    Procedures


29PART II 
    OTHER INFORMATION


30Item 1


Legal
    Proceedings


30Item 1A


Risk
    Factors


30Item 2


Unregistered
    Sales of Equity Securities and Use of Proceeds


32Item 3


Defaults Upon
    Senior Securities


33Item 4


Submission of
    Matters to a Vote of Security Holders


33Item 5


Other
    Information


33Item 6


Exhibits


33SIGNATURES


34EXHIBIT 10.6EXHIBIT 10.7EXHIBIT 10.8EXHIBIT 31.1EXHIBIT 31.2EXHIBIT 32.1   2




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##### Table of Contents



PART 1 
    FINANCIAL INFORMATION  ITEM 1.
    CONSOLIDATED
    FINANCIAL STATEMENTS  BIOMED
    REALTY TRUST, INC.
 CONSOLIDATED BALANCE SHEETS
    (In thousands, except share data)  September 30, 2006


December 31, 2005(Unaudited)ASSETSInvestments in real estate, net

$
1,894,489


$
1,129,371Investment in unconsolidated
    partnership


2,445



2,483Cash and cash equivalents


47,318



20,312Restricted cash


6,100



5,487Accounts receivable, net


4,616



9,873Accrued straight-line rents, net


16,576



8,731Acquired above market leases, net


8,018



8,817Deferred leasing costs, net


127,141



136,640Deferred loan costs, net


12,001



4,855Prepaid expenses


5,981



2,164Other assets


14,661



8,577Total assets

$
2,139,346


$
1,337,310LIABILITIES AND
    STOCKHOLDERS EQUITYMortgage notes payable, net

$
389,407


$
246,233Secured term loan


250,000



250,000Unsecured exchangeable notes


175,000



Unsecured line of credit






17,000Security deposits


6,556



6,905Dividends and distributions payable


19,823



13,365Accounts payable, accrued
    expenses, and other liabilities


34,565



23,012Acquired below market leases, net


26,312



29,647Total liabilities


901,663



586,162Minority interests


19,596



20,673Stockholders equity:Preferred stock, $.01 par
    value, 15,000,000 shares authorized, none issued or
    outstanding






Common stock, $.01 par value,
    100,000,000 shares authorized, 65,493,232 and
    46,634,432 shares issued and outstanding at
    September 30, 2006 and December 31, 2005, respectively


655



466Additional paid-in capital


1,271,213



757,591Accumulated other comprehensive
    income


6,435



5,922Dividends in excess of earnings


(60,216
)


(33,504
)Total stockholders equity


1,218,087



730,475Total liabilities and
    stockholders equity

$
2,139,346


$
1,337,310    3




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##### Table of Contents



BIOMED
    REALTY TRUST, INC.
 CONSOLIDATED
    STATEMENTS OF INCOME
    (In thousands, except per share data)  For the Three Months Ended


For the Nine Months EndedSeptember 30,


September 30,2006


2005


2006


2005(Unaudited)


(Unaudited)Revenues:Rental

$
49,758


$
28,593


$
117,492


$
62,821Tenant recoveries


14,743



12,225



40,191



28,035Other income


9



512



79



3,508Total revenues


64,510



41,330



157,762



94,364Expenses:Rental operations


11,128



9,763



30,313



22,879Real estate taxes


5,736



3,573



14,564



7,836Depreciation and amortization


18,618



12,164



46,694



26,832General and administrative


4,609



3,756



13,162



9,001Total expenses


40,091



29,256



104,733



66,548Income from operations


24,419



12,074



53,029



27,816Equity in net income of
    unconsolidated partnership


20



20



62



91Interest income


218



807



813



987Interest expense


(13,346
)


(7,422
)


(30,383
)


(15,645
)Income before minority interests


11,311



5,479



23,521



13,249Minority interests in consolidated
    partnerships


15



45



115



219Minority interests in operating
    partnership


(514
)


(323
)


(1,192
)


(991
)Net income

$
10,812


$
5,201


$
22,444


$
12,477Basic earnings per share

$
0.18


$
0.11


$
0.42


$
0.34Diluted earnings per share

$
0.18


$
0.11


$
0.42


$
0.34Weighted-average common shares
    outstanding:Basic


60,477,672



46,287,617



52,822,498



36,406,068Diluted


63,646,647



49,444,409



55,926,343



39,545,665    4




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##### Table of Contents



BIOMED
    REALTY TRUST, INC.
 CONSOLIDATED STATEMENTS OF CASH FLOWS

(In thousands)  Nine Months Ended September 30,2006


2005(revised  Seenote 2)(Unaudited)Operating activities:Net income

$
22,444


$
12,477Adjustments to reconcile net income
    to net cash provided by operating activities:Depreciation and amortization


46,694



26,832Minority interests in consolidated
    partnerships


(115
)


(219
)Minority interests in operating
    partnership


1,192



991Bad debt expense


118



171Revenue reduction attributable to
    acquired above market leases


1,840



1,189Revenue recognized related to
    acquired below market leases


(3,588
)


(2,157
)Compensation expense related to
    restricted common stock


2,887



3,007Amortization of deferred loan costs


1,322



2,675Amortization of debt premium on
    mortgage notes payable


(1,837
)


(1,280
)Income from unconsolidated
    partnership


(62
)


(91
)Distributions received from
    unconsolidated partnership


100



69Changes in operating assets and
    liabilities:Restricted cash


(613
)


(3,396
)Accounts receivable


5,139



(4,153
)Accrued straight-line rents


(7,845
)


(3,860
)Deferred leasing costs


(1,507
)


(440
)Prepaid expenses


(3,817
)


(3,685
)Other assets


(531
)


193Due to affiliates






(53
)Security deposits


(668
)


683Accounts payable, accrued expenses
    and other liabilities


10,553



12,367Net cash provided by operating
    activities


71,706



41,320Investing activities:Purchases of interests in and
    additions to real estate and related intangible assets


(799,291
)


(534,640
)Minority interest investment in
    consolidated partnerships


337



564Receipts of master lease payments


454



1,664Security deposits received from
    prior owners of rental property


319



708Additions to non-real estate assets


(1,094
)


(384
)Funds held in escrow for
    acquisitions


(2,100
)


250Net cash used in investing
    activities


(801,375
)


(531,838
)Financing activities:Proceeds from common stock offering


528,784



340,256Proceeds from exercise of stock
    warrant


4,050



Payment of offering costs


(21,866
)


(16,676
)Payment of loan costs


(8,138
)


(6,192
)Line of credit proceeds


392,311



227,175Line of credit payments


(409,311
)


(227,175
)Secured term loan proceeds






250,000Unsecured term loan proceeds






100,000Unsecured term loan payments






(100,000
)Secured bridge loan proceeds


150,000



Secured bridge loan payments


(150,000
)


Exchangeable notes proceeds


175,000



Mortgage notes proceeds


147,000



Principal payments on mortgage
    notes payable


(3,990
)


(2,468
)Leasehold tenant improvement loan


(2,000
)


Note receivable repayments


24



Distributions to operating
    partnership unit holders


(2,434
)


(2,325
)Dividends paid


(42,755
)


(25,451
)Net cash provided by financing
    activities


756,675



537,144Net increase in cash and cash
    equivalents


27,006



46,626Cash and cash equivalents at
    beginning of period


20,312



27,869Cash and cash equivalents at end of
    period

$
47,318


$
74,495Supplemental disclosure of cash
    flow information:Cash paid during the period for
    interest (net of amounts capitalized of $1,284 and $446,
    respectively)

$
29,814


$
12,827Supplemental disclosure of non-cash
    activities:Accrual for dividends declared


18,993



12,592Accrual for distributions declared
    for operating partnership unit holders


830



775Mortgage loans assumed (includes
    premium of $236 and $11,312, respectively)


2,001



149,516Accrued additions to real estate
    and related intangible assets


5,270



4,983    5




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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  Form 10-K
  Principles
    of Consolidation
    Investments
    in Partnerships
  Consolidation of Variable Interest Entities Consolidated
    Financial Statements The Equity
 6




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##### Table of Contents



BIOMED
    REALTY TRUST, INC.
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  Method of Accounting for Investments in Common Stock No. 04-5, 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 (EITF 04-5).
    EITF 04-5 states EITF 04-5
      Investments
    in Real Estate
    September 30, 2006


December 31, 2005Land

$
280,444


$
146,421Ground lease


14,210



14,210Buildings and improvements


1,553,967



962,482Construction in progress


48,001



8,582Tenant improvements


46,961



19,5801,943,583



1,151,275Accumulated depreciation


(49,094
)


(21,904
)$
1,894,489


$
1,129,371    7




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##### Table of Contents



BIOMED
    REALTY TRUST, INC.
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    September 30,


December 31,2006


2005Acquired above market leases

$
11,920


$
10,879Accumulated amortization


(3,902
)


(2,062
)$
8,018


$
8,817     September 30,


December 31,2006


2005Acquired below market leases

$
33,483


$
33,230Accumulated amortization


(7,171
)


(3,583
)$
26,312


$
29,647   Impairment
    of Long-Lived Assets and Long-Lived Assets to be
    Disposed
    Deferred
    Leasing Costs
      Balance atSeptember 30,


Accumulated2006


Amortization


NetAcquired in-place leases

$
157,411


$
(40,346
)

$
117,065Acquired management agreements


10,998



(3,993
)


7,005Deferred leasing and other direct
    costs


3,641



(570
)


3,071$
172,050


$
(44,909
)

$
127,141  8




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##### Table of Contents



BIOMED
    REALTY TRUST, INC.
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    Balance atDecember 31,


Accumulated2005


Amortization


NetAcquired in-place leases

$
149,312


$
(22,577
)

$
126,735Acquired management agreements


10,717



(2,505
)


8,212Deferred leasing and other direct
    costs


2,026



(333
)


1,693$
162,055


$
(25,415
)

$
136,640   Revenue
    Recognition
    Reporting Revenue Gross as a
    Principal versus Net as an Agent
    Incentive
    Awards
  Share-Based Payment Accounting for Stock-Based
    Compensation
   9




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##### Table of Contents



BIOMED
    REALTY TRUST, INC.
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  Managements
    Estimates
      Reclassifications
    Revisions
    to Consolidated Statements of Cash Flows
    3.
    Minority
    Interests  one-for-one
 10




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##### Table of Contents



BIOMED
    REALTY TRUST, INC.
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    4.
    Stockholders
    Equity              Accumulated
    Other Comprehensive Income
    Nine MonthsThree Months Ended


EndedSeptember 30,


September 30,2006


2005


2006


2005Net income


10,812



5,201



22,444



12,477Unrealized gain/(loss) on interest
    rate swap agreements


(5,211
)


5,567



513



3,802Comprehensive income/(loss)


5,601



10,768



22,957



16,279  11




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##### Table of Contents



BIOMED
    REALTY TRUST, INC.
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  5.
    Mortgage
    Notes Payable    StatedFixed

Effective

Principal BalanceInterest

Interest

September 30,


December 31,Rate

Rate

2006


2005


Maturity DateArdentech Court

7.25%

5.06%

$
4,681


$
4,746


July 1, 2012Bayshore Boulevard

4.55%

4.55%


15,826



16,107


January 1, 2010Bridgeview Technology Park I

8.07%

5.04%


11,653



11,732


January 1, 2011Eisenhower Road

5.80%

4.63%


2,176



2,211


May 5, 2008Elliott Avenue

7.38%

4.63%


16,150



16,526


November 24, 200740 Erie Street

7.34%

4.90%


18,928



19,575


August 1, 2008Kendall Square D

6.38%

5.45%


71,330



72,395


December 1, 2018Lucent Drive

5.50%

5.50%


5,779



5,899


January 21, 2015Monte Villa Parkway

4.55%

4.55%


9,634



9,805


January 1, 2010Nancy Ridge Drive

7.15%

5.38%


6,893



6,952


September 1, 2012Science Center Drive

7.65%

5.04%


11,479



11,577


July 1, 2011Shady Grove Road

5.97%

5.97%


147,000






September 1, 2016Sidney Street

7.23%

5.11%


30,910



31,426


June 1, 2012Towne Centre Drive

4.55%

4.55%


22,005



22,396


January 1, 2010900 Uniqema Boulevard

8.61%

5.61%


1,681






May 1, 2015376,125



231,347Unamortized premium






13,282



14,886$
389,407


$
246,233       6.
    Credit
    Facilities, Exchangeable Notes, and Other Debt
    Instruments     12




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##### Table of Contents



BIOMED
    REALTY TRUST, INC.
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
         13




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##### Table of Contents



BIOMED
    REALTY TRUST, INC.
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
        2006

$
1,4122007


21,3462008


24,2272009


4,7832010


297,186Thereafter


452,171$
801,125   7.
    Earnings
    Per Share   14




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##### Table of Contents



BIOMED
    REALTY TRUST, INC.
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    Earnings per Share
  For the Three Months Ended


For the Nine Months EndedSeptember 30,


September 30,2006


2005


2006


2005Net income attributable to common
    shares

$
10,812


$
5,201


$
22,444


$
12,477Minority interests in operating
    partnership


514



323



1,192



991Adjusted net income attributable
    to common shares

$
11,326


$
5,524


$
23,636


$
13,468Weighted-average common shares
    outstanding:Basic


60,477,672



46,287,617



52,822,498



36,406,068Incremental shares from assumed
    conversion/exercise:Stock warrant


136,306



103,123



127,926



87,038Vesting of restricted stock


169,105



183,105



112,355



181,995Operating partnership units


2,863,564



2,870,564



2,863,564



2,870,564Diluted


63,646,647



49,444,409



55,926,343



39,545,665Earnings per share 
    basic

$
0.18


$
0.11


$
0.42


$
0.34Earnings per share 
    diluted

$
0.18


$
0.11


$
0.42


$
0.34     8.
    Incentive
    Award Plan     15




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##### Table of Contents



BIOMED
    REALTY TRUST, INC.
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
        WeightedUnvested


Average Grant-Restricted Shares


Date Fair ValueBalance at January 1, 2006


344,492


$
17.70Granted


147,200



27.11Vested


(153,194
)


16.53Balance at March 31, 2006


338,498


$
22.32Granted


11,000



28.53Vested


(10,000
)


21.20Forfeited


(150
)


26.70Balance at June 30, 2006


339,348


$
22.55Granted


2,000



31.02Balance at September 30, 2006


341,348


$
22.60   WeightedUnvested


Average Grant-Restricted Shares


Date Fair ValueBalance at January 1, 2005


336,333


$
15.03Granted


46,225



20.24Vested


(109,440
)


15.03Balance at March 31, 2005


273,118


$
15.91Granted


12,000



21.09Balance at June 30, 2005


285,118


$
16.13Granted


71,449



23.85Vested


(8,000
)


15.00Forfeited


(2,617
)


20.28Balance at September 30, 2005


345,950


$
17.72   9.
    Segment
    Information   16




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##### Table of Contents



BIOMED
    REALTY TRUST, INC.
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  Disclosures about Segments of an Enterprise and Related
    Information
    10.
    Property
    Acquisitions    AquiredAbove


Deferred Leasing Costs


Acquired Below


Mortgage


Mortgage


TotalAcquisition


Investments


Market


In Place


Management


Market


Note


Note


CashProperty

Date


in Real Estate


Lease


Lease


Fee


Lease


Assumed


Premium


ConsiderationFairview Avenue


1/12/2006


$
2,703


$



$



$



$



$



$



$
2,703900 Uniqema Boulevard


1/13/2006



4,106



700



310











(1,766
)


(236
)


3,11458 Charles Street


4/7/2006



12,033



327



1,043







(178
)










13,225Belward Campus Drive


5/24/2006



200,966



























200,966Shady Grove Road


5/24/2006



226,080



























226,080One Research Way


5/31/2006



8,484



























8,484Ardenwood Venture


6/14/2006



13,949







313



10



(74
)










14,198Walnut Street


7/7/2006



41,266







3,634



180















45,080Pacific Research Center


7/11/2006



216,401



























216,401Spring Mill Drive


7/20/2006



8,950



13



852



















9,815Trade Centre Avenue


8/9/2006



18,675







1,947



92















20,714John Hopkins Court


8/16/2006



23,086



























23,086$
776,699


$
1,040


$
8,099


$
282


$
(252
)

$
(1,766
)

$
(236
)

$
783,866Weighted average intangible
    amortization life (in months)










83



95



116



20







112



    17




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##### Table of Contents



BIOMED
    REALTY TRUST, INC.
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    11.
    Derivatives
    and Other Financial Instruments           18




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##### Table of Contents



BIOMED
    REALTY TRUST, INC.
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
          12.
    New
    Accounting Standards  Accounting for Uncertainty in Income Taxes, an Interpretation
    of FASB Statement No. 109
 19




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##### Table of Contents



BIOMED
    REALTY TRUST, INC.
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  Fair Value Measurements
  Considering the
    Effects of Prior Year Misstatements when Quantifying
    Misstatements in Current Year Financial Statements
  13.
    Subsequent
    Events     20




---



##### Table of Contents



ITEM 2.
    MANAGEMENTS
    DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF
    OPERATIONS    Form 10-K Form 10-Q
  Overview
     21




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##### Table of Contents



Factors
    Which May Influence Future Operations
      Critical
    Accounting Policies
  Form 10-K
  Share-Based Payment Accounting for Stock-Based
    Compensation
    New
    Accounting Standards
  Accounting for Uncertainty in Income Taxes, an Interpretation
    of FASB Statement No. 109
 22




---



##### Table of Contents



Fair Value Measurements
  Considering the
    Effects of Prior Year Misstatements when Quantifying
    Misstatements in Current Year Financial Statements
  Results
    of Operations
  Comparison
    of Three Months Ended September 30, 2006 to the Three
    Months Ended September 30, 2005
  Rental Revenues.
  Tenant Recoveries.
  Other Income.
  Rental Operations Expense.
  Real Estate Tax Expense.
  Depreciation and Amortization
    Expense.
 23




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##### Table of Contents



General and Administrative Expenses.
  Interest Income.
  Interest Expense.
  Minority Interests in Consolidated
    Partnerships.
  Minority Interests in Operating
    Partnership.
  Comparison
    of Nine Months Ended September 30, 2006 to the Nine Months
    Ended September 30, 2005
  Rental Revenues.
  Tenant Recoveries.
  Other Income.
  Rental Operations Expense.
 24




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##### Table of Contents



Real Estate Tax Expense.
  Depreciation and Amortization
    Expense.
  General and Administrative Expenses.
  Interest Income.
  Interest Expense.
  Minority Interests in Consolidated
    Partnerships.
  Minority Interests in Operating
    Partnership.
  Cash
    Flows
  Comparison
    of Nine Months Ended September 30, 2006 to Nine Months
    Ended September 30, 2005
  Nine Months Ended September 30,2006


2005


Change(In thousands)Net cash provided by operating
    activities

$
71,706


$
41,320


$
30,386Net cash used in investing
    activities


(801,375
)


(531,838
)


(269,537
)Net cash provided by financing
    activities


756,675



537,144



219,531Ending cash balance


47,318



74,495



(27,177
)  25




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Funds
    from Operations
   26




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##### Table of Contents



For the Three Months Ended September 30,


For the Nine Months Ended September 30,2006


2005


2006


2005Net income

$
10,812


$
5,201


$
22,444


$
12,477AdjustmentsMinority interests in operating
    partnership


514



323



1,192



991Depreciation and
    amortization  real estate assets


18,638



12,184



46,754



26,862Funds from operations

$
29,964


$
17,708


$
70,390


$
40,330Funds from operations per
    share  diluted

$
0.47


$
0.36


$
1.26


$
1.02Weighted-average common shares
    outstanding  diluted


63,646,647



49,444,409



55,926,343



39,545,665   Liquidity
    and Capital Resources
    
    interest expense and scheduled principal payments on outstanding
    indebtedness,
    general and administrative expenses,
    future distributions expected to be paid to our
    stockholders, and
    capital expenditures, tenant improvements and leasing
    commissions.             27




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Off
    Balance Sheet Arrangements
      Cash
    Distribution Policy
  i.e.
   28




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Inflation
      ITEM 3.
    QUANTITATIVE
    AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK        ITEM 4.
    CONTROLS
    AND PROCEDURES   29




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Rule 13a-15(b),
   PART II 
    OTHER INFORMATION  ITEM 1.
    LEGAL
    PROCEEDINGS    ITEM 1A.
    RISK
    FACTORS  Form 10-K Form 10-Q Form 10-K Form 10-Q Form 10-K Form 10-Q, Form 10-K, Form 10-Q
  Risks
    Related to Our Properties, Our Business and Our Growth
    Strategy
  Because
    we lease our properties to a limited number of tenants, and to
    the extent we depend on a limited number of tenants in the
    future, the inability of any single tenant to make its lease
    payments could adversely affect our business and our ability to
    make distributions to our stockholders.
   30




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##### Table of Contents



The
    geographic concentration of our properties in Boston, Maryland
    and California makes our business particularly vulnerable to
    adverse conditions affecting these markets.
    Risks
    Related to Our Organizational Structure
  Conflicts
    of interest could result in our management acting other than in
    our stockholders best interests.
  Our executive officers and directors beneficially own 4.6% of
    our common stock and exercise substantial influence over our
    business and, as a result, they may delay, defer or prevent us
    from taking actions that would be beneficial to our other
    stockholders.
  Risks
    Related to Our Capital Structure
  Debt
    obligations expose us to increased risk of property losses and
    may have adverse consequences on our business operations and our
    ability to make distributions.
    
    Required payments of principal and interest may be greater than
    our cash flow from operations.
    We may be forced to dispose of one or more of our properties,
    possibly on disadvantageous terms, to make payments on our debt.
    If we default on our debt obligations, the lenders or mortgagees
    may foreclose on our properties that secure those loans.
    Further, if we default under a mortgage loan, we will
    automatically be in default on any other loan that has
    cross-default provisions, and we may lose the properties
    securing all of these loans.
    A foreclosure on one of our properties will be treated as a sale
    of the property for a purchase price equal to the outstanding
    balance of the secured debt. If the outstanding balance of the
    secured debt exceeds our tax basis in the property, we would
    recognize taxable income on foreclosure without realizing any
    accompanying cash proceeds to pay the tax (or to make
    distributions based on REIT taxable income).
    We may not be able to refinance or extend our existing debt. If
    we cannot repay, refinance or extend our debt at maturity, in
    addition to our failure to repay our debt, we may be unable to
    make distributions to our stockholders at expected levels or at
    all. 31




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##### Table of Contents




    Even if we are able to refinance or extend our existing debt,
    the terms of any refinancing or extension may not be as
    favorable as the terms of our existing debt. If the refinancing
    involves a higher interest rate, it could adversely affect our
    cash flow and ability to make distributions to stockholders.    Risks
    Related to Our REIT Status
  The
    number of shares of our common stock available for future sale
    could adversely affect the market price of our common
    stock.
        
    sales of substantial amounts of shares of our common stock in
    the public market, or the perception that such sales might occur,
    the exchange of units for common stock,
    the exercise of any options granted to certain directors,
    executive officers and other employees under our incentive award
    plan,
    issuances of preferred stock with liquidation or distribution
    preferences, and
    other issuances of our common stock.      ITEM 2.
    UNREGISTERED
    SALES OF EQUITY SECURITIES AND USE OF PROCEEDS   32




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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 Exhibit4
.1

Indenture, dated
    September 25, 2006, among BioMed Realty, L.P., BioMed
    Realty Trust, Inc. and U.S. Bank National Association, as
    trustee, including the form of 4.50% Exchangeable Senior Notes
    due 2026.(1)10
.1

Promissory Note, dated
    August 23, 2006, by BMR-Shady Grove B LLC in favor of
    KeyBank National Association.(2)10
.2

Indemnity Deed of Trust,
    Assignment of Leases and Rents, Security Agreement, and Fixture
    Filing, dated August 23, 2006, by BMR-Shady Grove Road HQ
    LLC in favor of KeyBank National Association.(2)10
.3

First Amendment to Employment
    Agreement between BioMed Realty Trust, Inc. and Gary A. Kreitzer
    dated as of September 15, 2006.(3)10
.4

Registration Rights Agreement,
    dated September 25, 2006, among BioMed Realty Trust, Inc.,
    BioMed Realty, L.P., Credit Suisse Securities (USA) LLC and
    Morgan Stanley & Co. Incorporated.(1)10
.5

Real Estate Purchase and Sale
    Agreement, dated as of October 20, 2006, among BioMed
    Realty, L.P., CLSB I, LLC and CLSB II, LLC.(4)10
.6

First Amendment to Real Estate
    Purchase and Sale Agreement, dated as of November 2, 2006,
    among BioMed Realty, L.P., CLSB I, LLC and CLSB II,
    LLC.10
.7

First Amendment to First Amended
    and Restated Unsecured Credit Agreement, dated as of
    November 3, 2006, by and among BioMed Realty, L.P., KeyBank
    National Association, as Administrative Agent, and certain
    lenders party thereto.10
.8

Second Amendment to Secured Term
    Loan Agreement, dated as of November 3, 2006, by and among
    BioMed Realty, L.P., KeyBank National Association, as
    Administrative Agent, and certain lenders party thereto.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.     (1)
    
    Incorporated herein by reference to BioMed Realty Trust,
    Inc.s Current Report on
    Form 8-K
    filed with the Securities and Exchange Commission on
    September 26, 2006.(2)
    
    Incorporated herein by reference to BioMed Realty Trust,
    Inc.s Current Report on
    Form 8-K
    filed with the Securities and Exchange Commission on
    August 28, 2006.(3)
    
    Incorporated herein by reference to BioMed Realty Trust,
    Inc.s Current Report on
    Form 8-K
    filed with the Securities and Exchange Commission on
    September 15, 2006.(4)
    
    Incorporated herein by reference to BioMed Realty Trust,
    Inc.s Current Report on
    Form 8-K
    filed with the Securities and Exchange Commission on
    October 24, 2006. 33




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SIGNATURES      ALAN
    D. GOLD
        KENT
    GRIFFIN
         34