Exhibit 1.1

JUNE [  ], 2001

Private & Confidential

Mr. Stephen Cohen
Chief Financial Officer
Genome Therapeutics Corporation
100 Beaver Street
Waltham, MA  02154-8440

Ladies and Gentlemen:

Reference is made to the registration statement on Form S-3 (No. 333-32614)
together with all amendments thereto (the "Registration Statement") filed by
Genome Therapeutics Corporation (the "Company") with the Securities and Exchange
Commission under the Securities Act of 1933, as amended (the "Securities Act"),
to register the resale of 1,950,000 shares of common stock, $0.10 par value, of
the Company (the "Registered Shares") by the Company.

The Company has engaged Tucker Anthony Sutro as its non-exclusive agent
(hereinafter "Agent") in connection with sales of the Registered Shares under
the Registration Statement (the "Transaction"). The terms of this engagement are
as follows:

The Agent hereby agrees that it will distribute copies of the prospectus,
including any amendment thereof or supplement thereto (the "Prospectus") in
connection with the sale of the Registered Shares in strict compliance with the
prospectus delivery requirements under the Securities Act. The Agent also
warrants that all Registered Shares will be sold in accordance with the section
of the Registration Statement entitled "Plan of Distribution."

The Company hereby agrees to indemnify, to the extent permitted by law, the
Agent, its officers and directors and each person who controls (within the
meaning of the Securities Act) such Agent (each an "Indemnified Party") against
all losses, claims, damages, liabilities and expenses caused by any untrue or
alleged untrue statement of material fact contained in the Registration
Statement, any prospectus or preliminary prospectus included as a part thereof
or any amendment thereof or supplement thereto or any omission or alleged
omission of a material fact required to be stated therein or necessary to make
the statements therein not misleading, except insofar as the same are caused by
or contained in any information furnished in writing to the Company by the Agent
expressly for use therein or by the Agent's failure to deliver a copy of the
Registration Statement or prospectus or any amendments or supplements thereto.
The Company's indemnification with respect to any preliminary prospectus shall
not inure to the benefit of any Indemnified Party or any person controlling such
Indemnified Party, if a copy of the Prospectus (as then amended or supplemented
if the Company shall have furnished any amendments or supplements thereto) was
not sent or given by or on behalf of such Indemnified Party to the person
asserting any such losses, claims, damages or liabilities, and if the Prospectus
(as so amended or supplemented) would have cured the defect giving rise to such
losses, claims, damages or liabilities.




Each Indemnified Party will (i) give prompt written notice to the Company of any
claim with respect to which it seeks indemnification (provided that failure to
give prompt notice shall not impair any Indemnified Party's right to
indemnification except to the extent such failure has prejudiced the Company)
and (ii) unless in such Indemnified Party's reasonable judgment a conflict of
interest between such Indemnified Party and the Company may exist with respect
to such claim, permit the Company to assume the defense of such claim with
counsel reasonably satisfactory to the Indemnified Party. The Company will not
be subject to any liability for any settlement made by the Indemnified Party
without its consent (but such consent will not be unreasonably withheld). The
Company need not pay the fees and expenses of more than one counsel for all
Indemnified Parties under this agreement with respect to such claim unless a
conflict of interest between the Indemnified Parties is apparent.

The indemnification provided for hereunder will remain in full force and effect
regardless of any investigation made by or on behalf of the Indemnified Party or
any officer, director or controlling person of such Indemnified Party and will
survive the transfer of the Registered Shares. The Company also agrees to make
such provisions, as are reasonably requested by any indemnified party, for
contribution to such party in the event the Company's indemnification in
unavailable for any reason.

For its services as agent, Tucker Anthony Sutro will be paid a commission equal
to not more than 3% of the aggregate sales price of the shares they sell. The
Company will pay legal, accounting and other fees and expenses related to the
offer and sale of the common stock contemplated by this prospectus in the amount
of $10,000 (the "Fee") upon completion of the Transaction by Tucker Anthony. The
Company shall also pay the Fee to Tucker Anthony in the event that the Company
terminates this agreement before Tucker Anthony is able to complete the
Transaction; PROVIDED, HOWEVER, that the Fee shall not be paid by the Company if
this agreement is terminated because of market conditions. The Company will
provide at least 100 prospectuses and supplements to the Agent that will be
delivered by the Agent to buyers.

The Company warrants and represents to its Agent that it is fully authorized to
conduct the subject transaction, and that its CFO, Stephen Cohen, is its duly
authorized agent to bind the Company. The Company further warrants that nothing
has come to its attention that has caused it to believe that as of its effective
date the Registration Statement, as amended, and as of the date of the
prospectus supplement, contained any untrue statement of a material fact or
omitted to state any material fact required to be stated therein or necessary to
make the statements therein, in the light of the circumstances under which they
were made, not misleading. The Agent warrants to keep any non-public information
provided to the Agent confidential until made public by the Company. The Company
reserves the right to terminate this agreement at any time upon written notice
to the Agent, provided that the indemnity provisions herein and any obligations
of the Company under this agreement with respect to the reimbursement of
expenses and the payment of fees owing prior to termination shall remain in
effect after such termination.

Please indicate your agreement to the foregoing by signing a counterpart of this
letter below.

Genome Therapeutics Corporation

By: __________________________
         Stephen Cohen
         Chief Financial Officer

Agreed and accepted this ___ day of  June 2001

TUCKER ANTHONY SUTRO

By:___________________________________
         Susan Rae Yerkey
         Vice President