FILED PURSUANT TO RULE 424(B)(5)
                               FILE NO. 333-32614
                   PROSPECTUS SUPPLEMENT DATED JUNE 28, 2001
                      (TO PROSPECTUS DATED JUNE 21, 2000).
                                1,950,000 SHARES
                           GENOME THERAPEUTICS CORP.
                                  COMMON STOCK

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This prospectus supplement relates to the offer of 1,950,000 shares of common
stock of Genome Therapeutics Corp. being offered for the account of Genome
Therapeutics Corp.

Genome Therapeutics will sell the shares offered by it through Tucker Anthony
Incorporated, which is a broker-dealer, in one or more transactions, including
at-the-market transactions, at prevailing market prices on the Nasdaq Stock
Market. Genome Therapeutics expects to sell the shares promptly after the date
of this prospectus supplement, subject to prevailing market conditions. Tucker
Anthony has agreed to act as agent for Genome Therapeutics in selling the stock,
but it has not committed to purchase any of the shares itself.

Genome Therapeutics' common stock is currently traded on the Nasdaq Stock Market
under the trading symbol "GENE." On June 27, 2001, the last sale price of the
common stock on that market was $14.20 per share.

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INVESTING IN THESE SECURITIES INVOLVES RISKS. SEE "RISK FACTORS" BEGINNING ON
PAGE 3 OF THE PROSPECTUS.

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NEITHER THE SECURITIES AND EXCHANGE COMMISSION NOR ANY STATE SECURITIES
COMMISSION HAS APPROVED OR DISAPPROVED OF THESE SECURITIES OR DETERMINED IF THIS
PROSPECTUS IS TRUTHFUL OR COMPLETE. ANY REPRESENTATION TO THE CONTRARY IS A
CRIMINAL OFFENSE.

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                                  THE OFFERING

                                            
Common stock offered.........................  1,950,000 shares

Common stock to be outstanding after the       24,429,651 shares
  offer......................................

Use of proceeds..............................  We intend to use the net proceeds from this
                                               offering to fund research and development
                                               activities, including investment in our
                                               emerging pharmacogenomics program and
                                               expansion of our infectious disease
                                               franchise, and for general corporate purposes
                                               including capital expenditures, working
                                               capital, possible acquisitions and other
                                               general purposes.

Nasdaq National Market symbol................  GENE



    The share amounts in the table above are based on the number of shares
outstanding at May 29, 2001 and exclude 3,320,693 shares of common stock
issuable upon exercise of outstanding options at a weighted average price of
$8.17 per share.

                        ABOUT THIS PROSPECTUS SUPPLEMENT

    You should read this prospectus supplement along with the accompanying
prospectus carefully before you invest. Both documents contain important
information you should consider when making your investment decision. This
prospectus supplement contains information about the common stock offered hereby
and the prospectus contains information about our securities generally. This
prospectus supplement may add, update or change information in the prospectus.
You should rely only on the information provided in this prospectus supplement,
the accompanying prospectus or incorporated by reference in the accompanying
prospectus. We have not authorized anyone to provide you with different
information.

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                              PLAN OF DISTRIBUTION

    We will sell the 1,950,000 shares offered by us through Tucker Anthony
Incorporated, from time to time in a series of transactions, including
at-the-market transactions, effected on the Nasdaq Stock Market. In offering the
shares, Tucker Anthony will act as our agent and use its reasonable best efforts
to find buyers for the shares. Tucker Anthony Incorporated is not obligated to
purchase any of the shares for its own account and we are not obligated to sell
all of the 1,950,000 shares.

    Under the rules of the SEC, Tucker Anthony is likely considered an
underwriter as a result of their actions as our agent. Accordingly, it will have
to comply with applicable prospectus delivery requirements and Regulation M
under the Securities Exchange Act. Regulation M may preclude Tucker Anthony from
making a market in our common stock during the offering of our shares. For its
services as agent, Tucker Anthony will be paid a commission equal to not more
than 3% of the aggregate sales price of the shares they sell.

    Should Tucker Anthony become a market maker in the Company's stock, during
the pendency of the offering it may engage in passive market making
transactions. Passive market making is allowed during the period when the rules
of the SEC would otherwise prohibit market activity by an underwriter
participating in this offering. A passive market maker must comply with
applicable volume and price limitations and must be identified as such. In
general, a passive market maker must display its bid at a price not in excess of
the highest independent bid for the common stock; but if all independent bids
are lowered below the passive market maker's bid, the passive market maker must
also lower its bid once it exceeds specified purchase limits. Net purchases by a
passive market maker on each day are limited to a specified percentage of the
passive market maker's average daily trading volume in the common stock during a
specified period and must be discontinued when such limit is reached. Tucker
Anthony is not required to engage in passive market making and may end passive
market making activities at any time.

    We will pay legal, accounting and other fees and expenses related to the
offer and sale of the common stock contemplated by this prospectus supplement in
the amount of $10,000.

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