1
                                  UNITED STATES

                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                                  ------------

                                    FORM 10-Q

[X]  QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF
           THE SECURITIES AND EXCHANGE ACT OF 1934

For The Quarterly Period Ended: May 26, 2001
                                ------------

                                       OR

[ ]  TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF
             THE SECURITIES EXCHANGE ACT OF 1934

For the Transition Period From ___ to ____

                           Commission File No: 0-10824
                                               --------

                            GENOME THERAPEUTICS CORP.

             (EXACT NAME OF REGISTRANT AS SPECIFIED IN ITS CHARTER)

        MASSACHUSETTS                                   04-2297484
---------------------------------          ------------------------------------
  (STATE OR OTHER JURISDICTION             (I.R.S. EMPLOYER IDENTIFICATION NO.)
OF INCORPORATION OR ORGANIZATION)

     100 BEAVER STREET, WALTHAM, MASSACHUSETTS           02453
     -----------------------------------------         ----------
     (ADDRESS OF PRINCIPAL EXECUTIVE OFFICES)          (ZIP CODE)

       REGISTRANT'S TELEPHONE NUMBER, INCLUDING AREA CODE: (781) 398-2300
                                                           --------------

     Indicate by check mark whether the registrant (1) has filed all reports
required to be filed by Section 13 or 15(d) of the Securities Exchange Act of
1934 during the preceding 12 months (or for such shorter period that the
registrant was required to file such reports), and (2) has been subject to such
filing requirements for the past 90 days. Yes _X_ No___

     Indicate the number of shares outstanding of each of the issuer's classes
of common stock, as of the latest practicable date.

         COMMON STOCK                                       22,671,955
        --------------                               ------------------------
        $.10 PAR VALUE                               Outstanding July 6, 2001
        --------------

   2

                    Genome Therapeutics Corp. and Subsidiary

           Index to Financial Information and Other Information

                                                                           Page
Part I

Financial Information (unaudited):

     Consolidated Condensed Balance Sheets as of                            3
         August 31, 2000 and May 26, 2001

     Consolidated Statements of Operations                                  4
         for the thirteen and thirty-nine week periods ended
         May 27, 2000 and May 26, 2001

     Consolidated Statements of Cash Flows for the                          5
         thirty-nine week periods ended May 27, 2000
         and May 26, 2001

     Notes to Consolidated Condensed Financial                              6-12
         Statements

     Management's Discussion and Analysis of Financial                     13-17
         Condition and Results of Operations

Part II
Other Information:

     Other Information                                                     18
     Signature                                                             19


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GENOME THERAPEUTICS CORP. AND SUBSIDIARY
CONSOLIDATED CONDENSED BALANCE SHEETS




------------------------------------------------------------------------------------
                                                         August 31,          May 26,
                                                               2000             2001

------------------------------------------------------------------------------------
                                                                   
Assets
Current Assets:
   Cash and cash equivalents                            $52,111,172      $20,201,979
   Marketable securities                                 22,348,841       35,224,741
   Interest receivable                                      574,603        1,202,354
   Accounts receivable                                      268,498          123,018
   Unbilled costs and fees                                  548,807          326,077
   Prepaid expenses and other current assets                383,929          919,283
                                                        -----------      -----------
        Total current assets                             76,235,850       57,997,452

Property and equipment, at cost:
   Laboratory and scientific equipment                   18,465,674       20,156,358
   Leasehold improvements                                 8,260,884        8,302,307
   Equipment and furniture                                1,114,195        1,181,486
                                                        -----------      -----------
                                                         27,840,753       29,640,151
   Less accumulated depreciation
       and amortization                                  14,392,805       16,751,751
                                                        -----------      -----------
                                                         13,447,948       12,888,400

Restricted cash                                             200,000          200,000
Long-term marketable securities                           1,224,184       17,556,398
Other assets                                                227,541          351,550
                                                        -----------      -----------
        Total assets                                    $91,335,523      $88,993,800
                                                        -----------      -----------

Liabilities and Shareholders' Equity
Current Liabilities:
   Accounts payable                                     $ 1,543,603      $ 1,750,737
   Accrued expenses                                       3,240,423        3,442,298
   Deferred revenue                                       3,013,847        4,228,916
   Current maturities of long-term obligations            4,719,604        4,918,171
                                                        -----------      -----------
        Total current liabilities                        12,517,477       14,340,122
Long-term obligations, net of current maturities          4,543,201        3,194,468
Shareholders' equity                                     74,274,845       71,459,210
                                                        -----------      -----------
        Total liabilities and shareholders' equity      $91,335,523      $88,993,800
                                                        -----------      -----------



See Notes to Consolidated Condensed Financial Statements.


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GENOME THERAPEUTICS CORP. AND SUBSIDIARY
CONSOLIDATED STATEMENTS OF OPERATIONS



--------------------------------------------------------------------------------------------------------------
                                                Thirteen Week Periods Ended    Thirty-Nine Week Periods Ended
                                                    May 27,          May 26,          May 27,          May 26,
                                                       2000             2001             2000             2001
                                                         (Unaudited)                     (Unaudited)
--------------------------------------------------------------------------------------------------------------
                                                                                      
Revenues:
  Contract research, licenses, and
    subscription fees                          $  6,477,526     $  6,411,899     $ 20,317,699     $ 20,213,733

Costs and Expenses:
  Research and development                     $  6,293,820     $  7,919,062     $ 18,043,366     $ 22,409,406
  Selling, general and administrative          $  1,322,611     $  1,887,613     $  4,010,560     $  5,314,816
                                               ------------     ------------     ------------     ------------
       Total costs and expenses                $  7,616,431     $  9,806,675     $ 22,053,926     $ 27,724,222

                                               ------------     ------------     ------------     ------------
Loss from Operations                           $ (1,138,905)    $ (3,394,776)    $ (1,736,227)    $ (7,510,489)
                                               ------------     ------------     ------------     ------------

  Interest income                              $    470,037     $  1,044,798     $  1,269,304     $  3,426,662
  Interest expense                             $   (220,188)    $   (193,722)    $   (616,639)    $   (587,996)
                                               ------------     ------------     ------------     ------------
       Net interest income                          249,849          851,076          652,665        2,838,666
                                               ------------     ------------     ------------     ------------

       Net loss                                $   (889,056)    $ (2,543,700)    $ (1,083,562)    $ (4,671,823)
                                               ------------     ------------     ------------     ------------

Net Loss per Common Share:
  Basic and diluted                            $      (0.04)    $      (0.11)    $      (0.05)    $      (0.21)
                                               ------------     ------------     ------------     ------------

Weighted average common shares outstanding:
  Basic and diluted                              20,606,918       22,434,920       19,799,349       22,356,317
                                               ------------     ------------     ------------     ------------



See Notes to Consolidated Financial Statements.


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GENOME THERAPEUTICS CORP. AND SUBSIDIARY
CONSOLIDATED STATEMENTS OF CASH FLOWS




------------------------------------------------------------------------------------------
                                                            Thirty-Nine Week Periods Ended
                                                                 May 27,           May 26,
                                                                    2000              2001
                                                                      (Unaudited)
------------------------------------------------------------------------------------------
                                                                          

Cash Flows from Operating Activities:
Net loss                                                    $ (1,083,562)      $(4,671,823)
Adjustments to reconcile net loss to net
  cash provided by operating activities:
    Depreciation and amortization                              2,969,060         3,336,831
    Loss on disposal of fixed assets                                  --           125,642
    Stock-based compensation expense                             696,568           995,951
    Changes in assets and liabilities:
      Interest receivable                                       (107,237)         (627,751)
      Accounts receivable                                       (364,263)          145,480
      Unbilled costs and fees                                     14,927           222,730
      Prepaid expenses and other current assets                 (419,730)         (535,354)
      Accounts payable                                           190,470           207,134
      Accrued expenses                                           841,426           201,875
      Deferred revenue                                           734,449         1,215,069
                                                            ------------      ------------
        Total adjustments                                      4,555,670         5,287,607
                                                            ------------      ------------

        Net cash provided by operating activities              3,472,108           615,784
                                                            ------------      ------------

Cash Flows from Investing Activities:
  Purchases of marketable securities                         (34,286,912)      (66,163,114)
  Maturities of marketable securities                         34,077,550        36,955,000
  Purchases of property and equipment                           (685,644)         (584,343)
  Increase in other assets                                      (467,769)         (124,009)
                                                            ------------      ------------

    Net cash used in investing activities                     (1,362,775)      (29,916,466)
                                                            ------------      ------------

Cash Flows from Financing Activities:
  Proceeds from sale of common stock                           3,732,115                --
  Proceeds from exercise of stock options                      3,759,507           733,047
  Proceeds from employee stock purchase plan                          --           124,790
  Proceeds from sale of restricted common stock                       --             2,400
  Payments on long-term obligations                           (3,205,517)       (3,468,748)
                                                            ------------      ------------

    Net cash provided by (used in) financing activities        4,286,105        (2,608,511)
                                                            ------------      ------------

Net Increase in Cash and Cash Equivalents                      6,395,438       (31,909,193)
Cash and Cash Equivalents, at beginning of period             12,802,162        52,111,172
                                                            ------------      ------------

Cash and Cash Equivalents, at end of period                 $ 19,197,600      $ 20,201,979
                                                            ------------      ------------

Supplemental Disclosure of Cash Flow Information:
  Interest paid during period                               $    616,639      $    587,996
                                                            ------------      ------------

  Income taxes paid during period                           $     10,800      $     20,250
                                                            ------------      ------------

Supplemental Disclosure of Non-cash Investing and
  Financing Activities:
  Equipment acquired under capital lease obligations        $  2,664,154      $  2,318,582
                                                            ------------      ------------



See Notes to Consolidated Condensed Financial Statements.


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NOTES TO CONSOLIDATED CONDENSED FINANCIAL STATEMENTS (UNAUDITED)

1.   BASIS OF PRESENTATION

          The consolidated condensed financial statements included herein have
been prepared by the Company, without audit, pursuant to the rules and
regulations of the Securities and Exchange Commission. In the opinion of
management, the unaudited consolidated condensed financial statements have been
prepared on the same basis as the audited consolidated financial statements and
include all adjustments (consisting only of normal recurring accruals) necessary
for a fair presentation of interim period results. Certain information and
footnote disclosures normally included in the financial statements prepared in
accordance with generally accepted accounting principles have been condensed or
omitted pursuant to such rules and regulations. The Company believes, however,
that its disclosures are adequate to make the information presented not
misleading. The results of operations for the thirty-nine week period ended May
26, 2001 are not necessarily indicative of the results to be expected for the
full fiscal year. The accompanying consolidated condensed financial statements
should be read in conjunction with the Company's Form 10-K, which was filed with
the Securities and Exchange Commission on November 22, 2000.

2.   REVENUE RECOGNITION

          Revenues consist of license fees, milestone payments, contract
research and subscription fees from the PathoGenome(TM) Database. These revenues
are derived from alliances with pharmaceutical companies, government grants and
contracts, and fees received from custom gene sequencing and analysis. Revenues
from contract research derived from alliances with pharmaceutical companies,
from government grants and contracts, and from custom gene sequencing and
analysis are recognized over the respective contract periods as the services are
provided. License fees are recognized ratably over the life of the alliance.
Subscription fees from the PathoGenome Database are recognized ratably over the
life of the subscription. Milestone payments from research and development
alliances are generally recognized when they are achieved. Unbilled costs and
fees represent revenue recognized prior to billing. Deferred revenue represents
amounts received prior to revenue recognition.

          Staff Accounting Bulletin (SAB) No. 101, Revenue Recognition, was
issued in December 1999 and must be adopted by companies no later than the
fourth quarter of fiscal year beginning after December 15, 1999. SAB No. 101
requires companies to recognize certain up-front nonrefundable fees over the
life of the related alliances when such fees are received in conjunction with
alliances that have multiple elements. The Company is required to adopt this new
accounting principles through a cumulative charge to its statement of
operations, in accordance with Accounting Principles Board (APB) Opinion No. 20,
Accounting Changes, no later than the fourth quarter of fiscal 2001. The Company
believes that the adoption of SAB No. 101 will not have a material impact on its
future operating results as it relates to the up-front nonrefundable payments
and milestone payments received in connection with alliances.

3.   NET LOSS PER COMMON SHARE

          The Company applies Statement of Financial Accounting Standards (SFAS)
No. 128, Earnings per Share, which establishes standards for computing and
presenting earnings per share. Basic and diluted earnings per share were
determined by dividing net loss by the weighted average common shares
outstanding during the period. Diluted loss per share is the same as basic loss
per share for all periods presented, as the effect of the potential common stock
is antidilutive. Antidilutive securities which consist of stock options,
restricted stock and directors' deferred stock that were not included in diluted
net loss per common share were 3,320,623 and 2,516,293 at May 26, 2001 and May
27, 2000, respectively.


                                       6
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4.   CASH, CASH EQUIVALENTS AND MARKETABLE SECURITIES

          The Company applies SFAS No. 115, Accounting for Certain Investments
in Debt and Equity Securities. At May 26, 2001 and August 31, 2000, the
Company's cash equivalents and marketable securities are classified as
held-to-maturity, as the Company has the positive intent and ability to hold
these securities to maturity. Cash equivalents are short-term, highly liquid
investments with original maturities of less than three months. Marketable
securities are investment securities with original maturities of greater than
three months. Cash equivalents are carried at cost, which approximates market
value, and consist of money market funds, repurchase agreements and debt
securities. Marketable securities are recorded at amortized cost, which
approximates market value. The Company has not recorded any realized gains or
losses on its marketable securities. Marketable securities consist of commercial
paper and U.S. government debt securities. The average maturity of the Company's
marketable securities is approximately 9 months at May 26, 2001.

At August 31, 2000 and May 26, 2001, the Company's cash, cash equivalents and
marketable securities consisted of the following:


                                             August 31,       May 26,
                                                 2000          2001
                                             -----------    -----------

Cash and Cash Equivalents:
  Cash ..................................    $42,211,172    $14,201,979
  Debt securities .......................      9,900,000    $ 6,000,000
                                             -----------    -----------
          Total cash and cash equivalents    $52,111,172    $20,201,979
                                             ===========    ===========
Marketable Securities:
  Short-term securities .................    $22,348,841    $35,224,741
                                             -----------    -----------
  Long-term securities ..................      1,224,184     17,556,398
                                             ===========    ===========
          Total marketable securities ...    $23,573,025    $52,781,139
                                             ===========    ===========

The Company has $200,000 in restricted cash in connection with certain long-term
obligations (see Note 8).

5.   USE OF ESTIMATES IN THE PREPARATION OF FINANCIAL STATEMENTS

          The preparation of financial statements in conformity with generally
accepted accounting principles requires management to make estimates and
assumptions that affect the reported amounts of assets and liabilities and
disclosure of contingent assets and liabilities at the date of the financial
statements and the reported amounts of revenues and expenses during the
reporting period. Actual results could differ from those estimates.

6.   COMPREHENSIVE LOSS

          The Company applies SFAS No. 130, Reporting Comprehensive Income. SFAS
No. 130 requires disclosure of all components of comprehensive income on an
annual and interim basis. Comprehensive income is defined as the change in
equity of a business enterprise during a period from transactions and other
events and circumstances from non-owner sources. The Company's total
comprehensive net loss for the thirteen and thirty-nine week periods ended May
26, 2001 and May 27, 2000 were the same as reported net loss for those periods.

7.   SEGMENT REPORTING

          The Company applies SFAS No. 131, Disclosures about Segments of an
Enterprise and Related Information. SFAS No. 131 establishes standards for
reporting information regarding operating segments in annual financial
statements and requires selected information for those segments to be


                                       7
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presented in interim financial reports issued to stockholders. SFAS No. 131 also
establishes standards for related disclosures about products and services and
geographic areas. Operating segments are identified as components of an
enterprise about which separate discrete financial information is available for
evaluation by the chief operating decision maker, or decision making group, in
making decisions how to allocate resources and assess performance. The Company's
chief decision makers, as defined under SFAS No. 131, are the chief executive
officer and chief financial officer. To date, the Company has viewed its
operations and manages its business as principally one operating segment. As a
result, the financial information disclosed herein represents all of the
material financial information related to the Company's principal operating
segment. All of the Company's revenues are generated in the United States and
all of its assets are located in the United States.

8.   LONG-TERM OBLIGATIONS

          On February 23, 2000, the Company entered into an equipment line of
credit under which it may finance up to $4,000,000 of laboratory, computer and
office equipment. On December 18, 2000, the Company increased the line of credit
by $3,000,000 to $7,000,000. The Company, at its discretion, can enter into
either an operating or capital lease. Borrowings under operating leases are
payable in 24 monthly installments and capital leases are payable in 36 monthly
installments. As of May 26, 2001, the Company has entered into $259,000 in
operating leases and $5,714,000 in capital leases. The interest rates under the
capital leases range from 7.55% to 10.37%. The Company had approximately
$1,027,000 available under this line of credit at May 26, 2001.

          The Company had entered into other capital lease arrangements under
which it financed approximately $15,060,000 of laboratory, computer and office
equipment, as well as facility renovations. These leases are payable in 36 to 48
monthly installments from date of initiation. Interest rates range from 7.63% to
10.28%. As of May 26, 2001, $3,668,000 was outstanding under these capital lease
arrangements. Under several agreements, we are required to maintain certain
financial ratios pertaining to minimum cash balances, tangible net worth and
debt service coverage. We had no additional borrowing capacity under these
capital lease agreements at May 26, 2001.

9.   ALLIANCES

(a) ASTRAZENECA

          In August 1995, the Company entered into a strategic alliance with
AstraZeneca (Astra), formerly Astra Hassle AB, to develop drugs, vaccines and
diagnostic products effective against peptic ulcers or any other disease caused
by H. pylori. The Company granted Astra exclusive access to the Company's H.
pylori genomic sequence database and exclusive worldwide rights to make, use and
sell products based on the Company's H. pylori technology. The agreement
provided for a four-year research alliance to further develop and annotate the
Company's H. pylori genomic sequence database, identify therapeutic and vaccine
targets and develop appropriate biological assays. In August 1999, the Company
successfully concluded its portion of the research alliance and transitioned the
program to AstraZeneca for pre-clinical testing.

          Under this agreement, Astra agreed to pay the Company subject to the
achievement of certain product development milestones, up to $23.3 million (and
possibly a greater amount if more than one product is developed under the
agreement) in license fees, expense allowances, research funding and milestone
payments. The Company received $13.5 million in license fees, expense
allowances, milestone payments and research funding under the Astra agreement
through May 26, 2001.

          The Company will also be entitled to receive royalties on Astra's sale
of products protected by the claims of patents licensed exclusively to Astra by
the Company pursuant to the agreement or the discovery of which was enabled in a
significant manner by the genomic database licensed to Astra by the Company. The
Company has the right, under certain circumstances, to convert Astra's license
to a nonexclusive license in the event that Astra is not actively pursuing
commercialization of the technology.


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     For the disclosed thirty-nine week periods ended May 26, 2001 and May 27,
2000, the Company recorded revenue of $0 and $22,000, respectively, under this
agreement.

     (b) SCHERING-PLOUGH

     In December 1995, the Company entered into a strategic alliance and license
agreement with Schering Corporation and Schering-Plough Ltd. (collectively,
Schering-Plough) providing for the use by Schering-Plough of the genomic
sequence of Staph. aureus to identify and validate new gene targets for
development of drugs to target Staph. aureus and other pathogens that have
become resistant to current antibiotics. As part of this agreement, the Company
granted Schering-Plough exclusive access to the Company's proprietary Staph.
aureus genomic sequence database. The Company also granted Schering-Plough a
nonexclusive license to use the Company's bioinformatics systems for
Schering-Plough's internal use in connection with the genomic databases licensed
to Schering-Plough under the agreement and other genomic databases
Schering-Plough develops or acquires. The Company also agreed to undertake
certain research efforts to identify bacteria-specific genes essential to
microbial survival and to develop biological assays to be used by
Schering-Plough in screening natural product and compound libraries to identify
antibiotics with new mechanisms of action.

     Under this agreement, Schering-Plough paid an initial license fee and will
fund the research program through at least September 2001. Under this agreement,
Schering-Plough agreed to pay the Company a minimum of $21.9 million in an
up-front license fee, research funding and milestone payments. Subject to the
achievement of additional product development milestones, Schering-Plough agreed
to pay the Company up to an additional $24 million in milestone payments.

     The agreement grants Schering-Plough exclusive worldwide rights to make,
use and sell pharmaceutical and vaccine products based on the genomic sequence
databases licensed to Schering-Plough by the Company and on the technology
developed in the course of the research program. The Company will be entitled to
receive royalties on Schering-Plough's sale of therapeutic products and vaccines
developed using the technology licensed from the Company. A total of $20.8
million has been received through May 26, 2001.

     For the thirteen-week periods ended May 26, 2001 and May 27, 2000, the
Company recorded revenue of $453,000 and $462,000, respectively, under this
agreement, which consisted of contract research revenue.

     For the thirty-nine week periods ended May 26, 2001 and May 27, 2000, the
Company recorded revenue of $1,280,000 and $1,581,000, respectively, under this
agreement, which consisted of contract research revenue.

     In December 1996, the Company entered into its second strategic alliance
and license agreement with Schering-Plough. This agreement calls for the use of
genomics to discover new pharmaceutical products for treating asthma. As part of
the agreement, the Company will employ its high-throughput disease gene
identification, bioinformatics, and genomics sequencing capabilities to identify
genes and associated proteins that can be utilized by Schering-Plough to develop
pharmaceuticals and vaccines for treating asthma. Under this agreement, the
Company has granted Schering-Plough exclusive access to (i) certain gene
sequence databases made available under this research program, (ii) information
made available to the Company under certain third-party research agreements,
(iii) an exclusive worldwide right and license to make, use and sell
pharmaceutical and vaccine products based on the rights to develop and
commercialize diagnostic products that may result from this alliance.

     Under this agreement, Schering-Plough paid an initial license fee and an
expense allowance to the Company. Schering-Plough agreed to fund the research
program through at least December 2001. In addition, upon completion of certain
scientific developments, Schering-Plough will make milestone payments, as well
as pay royalties based upon sales of therapeutics products developed from this
collaboration. If all milestones are met and the research program continues for
its full term, total payments to the Company will approximate $75.9 million,
excluding royalties. Of the total potential payments,


                                       9
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approximately $31.4 million represent license fees and research payments, and
$44.5 million represent milestone payments based on achievement of research and
product development milestones. A total of $32.0 million has been received
through May 26, 2001.

     For the thirteen-week periods ended May 26, 2001 and May 27, 2000, the
Company recorded revenue of $843,000 and $1,177,000, respectively, under this
agreement, which consisted of contract research revenue.

     For the thirty-nine week periods ended May 26, 2001 and May 27, 2000, the
Company recorded revenue of $4,059,000 and $4,934,000, respectively, under this
agreement, which consisted of contract research revenue and milestone payments.

     On September 1997, the Company entered into a third strategic alliance and
license agreement with Schering-Plough to use genomics to discover and develop
new pharmaceutical products to treat fungal infections.

     Under the agreement, the Company will employ its bioinformatics,
high-throughput sequencing and functional genomics capabilities to identify and
validate genes and associated proteins as drug discovery targets that can be
utilized by Schering-Plough to develop novel antifungal treatments.
Schering-Plough will receive exclusive access to the genomic information
developed in the alliance related to two fungal pathogens, Candida albicans and
Aspergillus fumigatus. Schering-Plough will also receive exclusive worldwide
right to make, use and sell products based on the technology developed during
the course of the research program. In return, Schering-Plough agreed to fund a
research program through at least September 2001. If all milestones are met and
the research program continues for its full term, total payments to the Company
will approximate $32.7 million, excluding royalties. Of the total potential
payments, $9.7 million represents contract research payments and $23.0 million
represents milestone payments based on achievement of research and product
development milestones. A total of $11.9 million has been received through May
26, 2001. Additionally, the Company entered into a subscription agreement with
Schering-Plough to provide Schering-Plough with nonexclusive access to the
Company's proprietary genome sequence database, PathoGenome and associated
information relating to microbial organisms (see Note 10).

     For the thirteen-week periods ended May 26, 2001 and May 27, 2000, the
Company recorded revenue of $394,000 and $577,000, respectively, under this
agreement, which consisted of contract research revenue.

     For the thirty-nine week period ended May 26, 2001, the Company recorded
revenue of $1,111,000 under this agreement, which consisted of contract research
revenue. For the thirty-nine week period ended May 27, 2000, the Company
recorded revenue of $2,852,000 under this agreement, which consisted of contract
research revenue and a milestone payment.

     (c) NATIONAL HUMAN GENOME RESEARCH INSTITUTE

     In July 1999, the Company was named as one of the nationally funded DNA
sequencing centers of the international Human Genome Project. The Company is
participating as part of an international consortium in a full-scale effort to
sequence the human genome. The Company is entitled to receive research and
development funding from the National Human Genome Research Institute (NHGRI) of
up to $15.6 million over a three-year period, of which $12.0 million is
appropriated through October 2001.

     In October 1999, the NHGRI named the Company as a pilot center to the Mouse
Genome Sequencing Network. The Company is entitled to receive $12.9 million in
funding over three years with respect to this agreement, of which $8.8 million
is appropriated through October 2001. In August 2000, the Company was named one
of two primary centers for the Rat Sequencing Program from NHGRI. As part of the
agreement, we will use remaining funding under the mouse award, as well as a
portion of the remaining funding under the human award to participate in this
rat genome initiative.


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   11

     For the thirteen-week periods ended May 26,2001 and May 27, 2000, the
Company recorded revenue of $3,079,000 and $1,958,000, respectively, under these
agreements. For the thirty-nine week periods ended May 26, 2001 and May 27,
2000, the Company recorded revenue of $7,810,000 and $5,113,000, respectively,
under these agreements.

     Funding under our government grants and research contracts is subject to
appropriation each year by the U.S. Congress and can be discontinued or reduced
at any time. In addition, we cannot be certain that we will receive additional
grants or contracts in the future.

     (d) BIOMERIEUX ALLIANCE

     In September 1999, the Company entered into a strategic alliance with
bioMerieux to develop, manufacture and sell in vitro diagnostic products for
human clinical and industrial applications. As part of the alliance, bioMerieux
purchased a subscription to the Company's PathoGenome Database (see Note 10),
paid an up-front license fee, agreed to fund a research program for at least
four years and pay royalties on future products. In addition, bioMerieux
purchased $3.75 million of the Company's common stock. The total amount of
research and development funding, excluding subscription fees, approximates $5.2
million for the four-year term of this agreement. The research and development
funding will be recognized ratably over the four-year term of the agreement.

     For the thirteen-week periods ended May 26, 2001 and May 27, 2000, the
Company recorded revenue of $297,000 and $430,000, respectively, under this
agreement, which consisted of contract research revenue and amortization of an
up-front license fee. For the thirty-nine week periods ended May 26, 2001 and
May 27, 2000, the Company recorded revenue of $891,000 and $949,000,
respectively, under this agreement, which consisted of contract research revenue
and amortization of an up-front license fee. A total of $2.7 million has been
received through May 26, 2001.

     (e) WYETH-AYERST LABORATORIES

     In December 1999, the Company entered into a strategic alliance with
Wyeth-Ayerst Laboratories to develop novel therapeutics for the prevention and
treatment of osteoporosis. The alliance will focus on developing therapeutics
utilizing targets based on the characterization of a gene associated with a
unique high bone mass trait.

     The agreement provides for the Company to employ its established
capabilities in positional cloning, bioinformatics and functional genomics in
conjunction with Wyeth-Ayerst's drug discovery capabilities and its expertise in
bone biology and the osteoporotic disease process to develop new
pharmaceuticals. Under the terms of the agreement, Wyeth-Ayerst paid the Company
an up-front license fee, and will fund a multi-year research program, which
includes milestone payments and royalties on sales of therapeutics products
developed from this alliance. If the research program continues for its full
term and substantially all of the milestone payments are met, total payments to
the Company, excluding royalties, would exceed $118 million.

     The Company recorded revenue of $375,000 for both thirteen-week periods
ended May 26, 2001 and May 27, 2000, under this agreement, which consisted of
contract research revenue and amortization of an up-front license fee. For the
thirty-nine week periods ended May 26, 2001 and May 27, 2000, the Company
recorded revenue of $1,250,000 and $625,000, respectively, under this agreement,
which consisted of contract research revenue and amortization of an up-front
license fee. A total of $2.6 million has been received through May 26, 2001. In
June 2001, subsequent to quarter-end, the Company received milestone payments of
$5.0 million for achieving certain research milestones.


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10.  DATABASE SUBSCRIPTIONS

          The Company has entered into a number of PathoGenomeTM Database
subscriptions. The database subscriptions provide nonexclusive access to the
Company's proprietary genome sequence database, PathoGenome Database, and
associated information relating to microbial organisms. These agreements call
for the Company to provide periodic data updates, analysis tools and software
support. Under the subscription agreements, the customer pays an annual
subscription fee and will pay royalties on any molecules developed as a result
of access to the information provided by the PathoGenome Database. The Company
retains all rights associated with protein therapeutic, diagnostic and vaccine
use of bacterial genes or gene products.

          For the thirteen-week periods ended May 26, 2001 and May 27, 2000, the
Company recorded revenue of $692,000 and $1,004,000, respectively, under these
agreements. For the thirty-nine week periods ended May 26, 2001 and May 27,
2000, the Company recorded revenue of $2,459,000 and $3,229,000, respectively,
under these agreements.


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                           MANAGEMENT'S DISCUSSION AND ANALYSIS OF
                  FINANCIAL CONDITION AND RESULTS OF OPERATIONS

OVERVIEW

     Genome Therapeutics Corp. ("GTC", "we", or "our") is a leader in the
commercialization of genomics-based drug discovery. We have over ten years of
experience in genomics research and have been one of the original recipients of
funding from the United States government under its genome programs. Our
commercial strategy is to use our genomics and related proprietary technologies
to identify and validate novel drug targets for commercialization. Our two areas
of scientific focus are the discovery and characterization of novel targets for
human diseases and infectious diseases. We also commercialize our sequencing
capabilities through the GTC Sequencing Center, which we established in July
1999 to provide high quality, industrial scale sequencing to pharmaceutical and
biotechnology companies on a fee for service basis. In May 1997, we introduced a
non-exclusive genetic database, the PathoGenome(TM) Database, which provides
subscribers with genetic information to identify gene targets. We believe that
our genomic discoveries and information from our database will lead to the
development of novel therapeutics, vaccines, and diagnostic products.

     We receive payments from our strategic partners based on license fees,
contract research and milestone payments during the term of the alliance. In
addition, subscribers to our PathoGenome Database pay access fees for the
information they obtain. Once a product resulting from a research alliance or a
subscriber's use of the PathoGenome Database is commercialized, we are entitled
to receive royalty payments based upon product revenues. We anticipate that our
alliances will result in the discovery and commercialization of novel
pharmaceutical, vaccine and diagnostic products. In order for a product to be
commercialized based on our research, it will be necessary for the strategic
partners to conduct preclinical tests and clinical trials, obtain regulatory
clearances, manufacture, sell, and distribute the product. Accordingly, we do
not expect to receive royalties based upon product revenues for many years, if
at all. Additionally, we sell, as a contract service business, high quality
genomic sequencing information to third parties, including pharmaceutical
companies, biotechnology companies, governmental agencies, and academic
institutions.

     Our primary sources of revenue are from alliance agreements with
pharmaceutical company partners, subscription agreements to our PathoGenome
Database and government research grants and contracts. Currently, we have seven
strategic research alliances. In August 1995, we entered into an alliance with
AstraZeneca to develop pharmaceutical, vaccine and diagnostic products effective
against gastrointestinal infections or any other disease caused by H. pylori. In
August 1999, the sponsored research under the alliance concluded and the program
transitioned into AstraZeneca's pipeline. We are entitled to receive additional
milestone payments and royalties based upon the development by AstraZeneca of
any products from the research alliance. We entered into an alliance with
Schering-Plough in December 1995. Under this alliance, Schering-Plough can use
our Staph. aureus genomic database to identify new gene targets for the
development of novel antibiotics. In December 1996, we entered into our second
research alliance with Schering-Plough to identify genes and associated proteins
that Schering-Plough can utilize to develop new pharmaceuticals for treating
asthma. In September 1997, we established our third research alliance with
Schering-Plough for the development of new pharmaceutical products to treat
fungal infections. In September 1999, we entered into a strategic alliance with
bioMerieux to develop, manufacture and sell in vitro pathogen diagnostic
products for human clinical and industrial applications. As part of the
strategic alliance, bioMerieux purchased a subscription to our PathoGenome
Database and made an equity investment. In December 1999, we entered into a
strategic alliance with Wyeth-Ayerst to develop drugs based on our genetic
research to treat osteoporosis.

     In May 1997, we introduced our PathoGenome Database and sold our first
subscription. Since that date, we have continued to contract with subscribers on
a non-exclusive basis, and, as of May 26, 2001, we had a total of seven
subscribers. Under our agreements, the subscribers receive non-exclusive access
to information relating to microbial organisms in our PathoGenome Database.
Subscriptions to the database generate revenue over the term of the subscription
with the potential for royalty payments to us from future product sales.


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     Since 1989, the United States government has awarded us a number of
research grants and contracts related to government genomics programs. The scope
of the research covered by grants and contracts encompasses technology
development, sequencing production, technology automation, and disease gene
identification. These programs strengthen our genomics technology base and
enhance the expertise of our scientific personnel. In July 1999, the government
named us as one of the nationally funded DNA sequencing centers of the
international Human Genome Project. We are participating in an international
consortium in a full-scale effort to sequence the human genome. We will receive
funding from the National Human Genome Research Institute (NHGRI) under the
Human Genome Project of up to $15.6 million over a three-year period, of which
$12.0 million is appropriated through October 2001. In October 1999, NHGRI
appointed us as one of the initial centers in the Mouse Genome Sequencing
Network. The NHGRI agreed to provide us with funding under this program of up to
$12.9 million over a three-year period, of which $8.8 million is appropriated
through October 2001. In August 2000, we were named as one of two primary
centers for the Rat Sequencing Program by NHGRI. As part of the agreement, we
switched our focus from the mouse genome to the rat genome and agreed to use all
remaining funding under the mouse genome award and a portion of the remaining
funding under the human genome award to participate in the rat genome
initiative. These programs are subject to annual appropriations by the
government based upon the availability of government funds and the achievement
by us of certain milestones.

     We have incurred significant operating losses since our inception. As of
May 26, 2001, we had an accumulated deficit of approximately $74.2 million. Our
losses are primarily from costs associated with prior operating businesses and
research and development expenses. These costs have often exceeded our revenues
generated by our alliances, subscription agreements and government contracts and
grants. Our results of operations have fluctuated from period to period and may
continue to fluctuate in the future based upon the timing, amount and type of
funding. We expect to incur additional operating losses in the future.

     We are subject to risks common to companies in our industry including
unproven technology and business strategy, reliance upon collaborative partners
and others, rapid technological change, history of operating losses, need for
future capital, competition, patent and proprietary rights, dependence on key
personnel, uncertainty of regulatory approval, uncertainty of pharmaceutical
pricing, healthcare reform and related matters, availability of, and competition
for, unique family resources, and volatility of our stock.

RESULTS OF OPERATIONS

THIRTEEN-WEEK PERIODS ENDED MAY 27, 2000 AND MAY 26, 2001

REVENUES

     Contract research, licenses, and subscription fees decreased 1% from
$6,478,000 for the thirteen-week period ended May 27, 2000 to $6,412,000 for the
thirteen-week period ended May 26, 2001. The decrease in contract research,
licenses and subscription fees was primarily attributable to a decline in
contract research revenue under our existing strategic alliances and lower
subscription fees to our PathoGenome Database. This decrease in revenue was
partially offset by an increase in revenue recognized under our GTC Sequencing
Center, which provides sequencing services for our biotechnology and
pharmaceutical customers, as well as for the National Human Genome Research
Institute as a participant in the International Human Genome Project and the Rat
Genome Sequencing projects.

COSTS AND EXPENSES

     Total costs and expenses increased 29% from $7,616,000 for the
thirteen-week period ended May 27, 2000 to $9,807,000 for the thirteen-week
period ended May 26, 2001. Research and development expense, which includes
internal research and development and research funded pursuant to arrangements
with our strategic alliances, commercial sequencing customers and the U.S.
government, increased 26% from $6,294,000 in the thirteen-week period ended May
27, 2000 to


                                       14
   15

$7,919,000 for the thirteen-week period ended May 26, 2001. The increase was
primarily due to an increase in costs and expenses associated with an expansion
of our internal research programs, specifically in the area of infectious
diseases, human gene discovery and pharmacogenomics. The increase consisted of
an increase in payroll and related expenses, laboratory supplies and overhead
expenses related to our operations.

     Selling, general and administrative expenses increased 43% from $1,323,000
for the thirteen-week period ended May 27, 2000 to $1,888,000 for the
thirteen-week period ended May 26, 2001. This increase was primarily
attributable to an increase in payroll related expenses, recruiting and employee
relocation expenses.

INTEREST INCOME AND EXPENSE

     Interest income increased 122% from $470,000 for the thirteen-week period
ended May 27, 2000 to $1,045,000 for the same period ended May 26, 2001,
reflecting primarily an increase in funds available for investment. The increase
in funds available for investment was primarily due to proceeds received last
year from the sale of common stock.

     Interest expense decreased 12% from $220,000 for thirteen-week period ended
May 27, 2000 to $194,000 for the same period ended May 26, 2001, due primarily
to a decrease in outstanding balances under our long-term obligations.

THIRTY-NINE-WEEK PERIODS ENDED MAY 27, 2000 AND MAY 26, 2001

REVENUES

     Contract research, licenses, and subscription fees decreased slightly from
$20,318,000 for the thirty-nine week period ended May 27, 2000 to $20,214,000
for the thirty-nine week period ended May 26, 2001. The slight decrease was
primarily attributable to a decline in contract research revenue, as well as
lower milestone payments earned this year in comparison to last year. These
decreases were equivalently offset by an increase in revenues derived from our
GTC Sequencing Center, specifically, from our government collaborations with the
National Human Genome Research Institute in participation of the International
Human Genome Project and the Rat Genome Sequencing projects.

COSTS AND EXPENSES

     Total costs and expenses increased 26% from $22,054,000 for the thirty-nine
week period ended May 27, 2000 to $27,724,000 for the thirty-nine week period
ended May 26, 2001. Research and development expense, which includes internal
research and development and research funded pursuant to arrangements with our
strategic alliances, commercial sequencing customers and the U.S. government,
increased by 24% from $18,043,000 for the thirty-nine week period ended May 27,
2000 to $22,409,000 for the thirty-nine week period ended May 26, 2001. The
increase was primarily attributable to an expansion of our internal research
programs, specifically in the area of infectious diseases, human gene discovery
and pharmacogenomics. The increase consisted of an increase in payroll and
related expenses, laboratory supplies and overhead expenses related to our
operations.

     Selling, general and administrative expenses increased 33% from $4,011,000
for the thirty-nine week period ended May 27, 2000 to $5,315,000 for the
thirty-nine week period ended May 26, 2001. This increase was primarily
attributable to an increase in payroll and related expenses and recruiting and
relocation expenses.


                                       15
   16

INTEREST INCOME AND EXPENSE

     Interest income increased 170% from $1,269,000 for the thirty-nine week
period ended May 27, 2000 to $3,427,000 for the same period ended May 26, 2001,
reflecting primarily an increase in funds available for investment. The increase
in funds available for investment was primarily due to proceeds received last
year from the sale of common stock.

     Interest expense decreased 5% from $617,000 for thirty-week period ended
May 27, 2000 to $588,000 for the same period ended May 26, 2001.

LIQUIDITY AND CAPITAL RESOURCES

     Our primary sources of cash have been payments received from strategic
alliances, subscription fees, government grants and contracts, borrowings under
equipment lending facilities and capital leases and proceeds from the sale of
equity securities.

     As of May 26, 2001, we had cash, cash equivalents, restricted cash, and
short-term and long-term marketable securities of approximately $73,183,000. In
fiscal 2000, we sold 1,500,000 shares of common stock in a series of
transactions through the NASDAQ National Market, resulting in net proceeds of
$44,723,000. During fiscal 2000, we issued 1,532,302 shares of common stock
related to the exercise of stock options, resulting in net proceeds of
approximately $4,155,000. In fiscal 2000, we also sold 678,610 shares of common
stock to bioMerieux, a strategic alliance partner, resulting in net proceeds of
approximately $3,732,000. For the thirty-nine week period ended May 26, 2001, we
issued 214,750 shares of common stock related to the exercise of stock options
and the employee stock purchase plan, resulting in proceeds received of
$858,000.

     We have various arrangements under which we financed certain office and
laboratory equipment and leasehold improvements. At May 26, 2001, we had an
aggregate of $8,113,000 outstanding under our borrowing arrangements, which are
repayable over the next 36 months, of which $4,918,000 is repayable within the
next 12 months. Under these arrangements, we are required to maintain certain
financial ratios, including minimum levels of tangible net worth, total
indebtedness to tangible net worth, minimum cash level, debt service coverage
and minimum restricted cash balances. As of May 26, 2001, the Company was in
compliance with all of these covenants. At May 26, 2001, we had approximately
$1,027,000 available under one of these arrangements for future borrowings.

     Our operating activities provided cash of $616,000 for the thirty-nine week
period ended May 26, 2001, primarily due to decrease in accounts receivable and
unbilled costs & fees, an increase in accounts payable, accrued expenses and
deferred revenue, as well as noncash expenditures such as depreciation and
amortization, stock-based compensation expense, and gain on disposal of fixed
assets. Cash provided by operations for the thirty-nine week period ended May
26, 2001 was partially offset by our net loss, and an increase in interest
receivable, prepaid expenses and other current assets.

     Our investing activities used cash of $29,916,000 for the thirty-nine week
period ended May 26, 2001 to purchase marketable securities, property and
equipment, partially offset by the conversion of marketable securities to cash
and cash equivalents. Our investing activities used cash of $1,363,000 for the
thirty-nine week period ended May 27, 2000 from the purchase of marketable
securities and property and equipment, partially offset by the conversion of
marketable securities to cash and cash equivalents.

     Capital expenditures, including property and equipment acquired under
capital leases, totaled $2,903,000 for the thirty-nine week period ended May 26,
2001. Purchases consisted primarily of laboratory and computer equipment. We
currently estimate that we will acquire an additional $3,097,000 in capital
equipment in fiscal 2001 consisting primarily of computer, laboratory equipment,
and additions to leasehold improvement. We intend to finance the majority of
capital purchases made during the fourth quarter of fiscal 2001 under existing
and new equipment financing arrangements, yet to be negotiated.

     Our financing activities used cash of $2,609,000 for the thirty-nine week
period ended May 26, 2001, primarily for payments of long-term obligations,
partially offset by proceeds received from the


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exercise of stock options and the sale of common stock under the employee stock
purchase plan. Our financing activities provided cash of approximately
$4,286,000 for the thirty-nine week period ended May 27, 2000, primarily from
the sale of equity securities, exercise of stock options, net of payments of
long-term obligations.

     At August 31, 2000, we had net operating loss and tax credits (investment
and research) carryforwards of $87,055,000 and $3,071,000, respectively,
available to reduce federal taxable income and federal income taxes,
respectively, if any. Net operating loss carryforwards are subject to review and
possible adjustment by the Internal Revenue Service and may be limited, in the
event of certain cumulative changes in ownership interests of significant
shareholders over a three-year period in excess of 50%. Additionally, certain of
these losses are expiring due to the limitations of the carryforwards period.

     We believe that under our current rate of investment in research and
development, our existing capital resources are adequate for the foreseeable
future. There is no assurance, however, that changes in our plans or events
affecting our operations will not result in accelerated, or unexpected
expenditures.

     We may seek additional funding in the future through public or private
financing. Additional financing may not be available when needed, or if
available, it may not be on terms acceptable to us. To the extent that we raise
additional capital by issuing equity or convertible debt securities, ownership
dilution to stockholders will result.

     We do not currently use derivative financial instruments. We generally
place our marketable security investments in high quality credit instruments, as
specified in our investment policy guidelines; the policy also limits the amount
of credit exposure to any one issue, issuer, and type of instrument. We do not
expect any material loss from our marketable security investments and therefore
believe that our potential interest rate exposure is limited.

     SAB No. 101 was issued in December 1999 and must be adopted by companies no
later than the fourth quarter of fiscal years beginning after December 15, 1999.
SAB No. 101 will require companies to recognize certain up-front nonrefundable
fees over the life of the related alliances when such fees are received in
conjunction with alliances that have multiple elements. The Company is required
to adopt this new accounting principles through a cumulative charge to its
statement of operations, in accordance with APB Opinion No. 20 no later than the
fourth quarter of fiscal 2001. The Company believes that the adoption of SAB No.
101 will not have a material impact on its future operating results as it
relates to the up-front nonrefundable payments and milestone payments received
in connection with alliances.

     This Form 10-Q and documents we have filed with the Securities and Exchange
Commission contain forward-looking statements made pursuant to the safe harbor
provisions of the Private Securities Litigation Reform Act of 1995.
Forward-looking statements represent our management's judgement regarding future
events. Forward-looking statements typically are identified by use of terms such
as "may," "will," "should," "plan," "expect," "intend," "anticipate,"
"estimate," and similar words, although some forward-looking statements are
expressed differently. All forward-looking statements, other than statements of
historical fact, included in this report regarding our financial position,
business strategy and plans or objectives for future operations are
forward-looking statements. We cannot guarantee the accuracy of the
forward-looking statements, nor do we plan to update these forward-looking
statements. You should be aware that our actual results could differ materially
from those contained in the forward looking statements due to a number of risks
affecting our business, including the ability of the Company and its alliance
partners to (i) successfully develop products based on the Company's genomic
information, (ii) obtain the necessary governmental approvals, (iii) effectively
commercialize any products developed before its competitors and (iv) obtain and
enforce intellectual property rights, as well as the risk factors set forth in
the Exhibit 99 to the Company's Annual Report on Form 10-K for the year ended
August 31, 2000 and those set forth in other filings that we may make with the
Securities and Exchange Commission from time to time.


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                                     Part II

Item 1. LEGAL PROCEEDINGS

     For a description of the lawsuit brought by Commonwealth Biotechnologies,
Inc. against the Company and other parties, see the Company's Quarterly Report
on Form 10-Q for quarter ended November 25, 2000.

Item 2. CHANGES IN SECURITIES

     None

Item 3. DEFAULTS UPON SENIOR SECURITIES

     None

Item 4. SUBMISSION OF MATTERS TO A VOTE OF SECURITY HOLDERS

     None

Item 5. OTHER INFORMATION

     None.

Item 6. EXHIBITS AND REPORTS ON FORM 8-K

     a)   EXHIBITS:

          None

     b)   Reports on Form 8-K

          None


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                                    Signature

Pursuant to the requirements of the Securities Exchange Act of 1934, the
registrant has caused this report to be signed on its behalf by the undersigned
thereunto duly authorized who also serves in the capacity of principal financial
officer.

                                 Genome Therapeutics Corp.

                                     /s/ Stephen Cohen
                                ---------------------------
                                 Stephen Cohen, SVP & CFO
                              (Principal Financial Officer)

                                   Date: July 10, 2001



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