EXHIBIT 99.2


                          GENOME THERAPEUTICS CORP.

                               100 Beaver Street
                               Waltham, MA 02453

              LETTER TO COMMISSION PURSUANT TO TEMPORARY NOTE 3T

                                March 29, 2002


Securities and Exchange Commission
450 Fifth Street, N.W.
Washington, D.C.  20549-0408

Ladies and Gentlemen:

Pursuant to Temporary Note 3T to Article 3 of Regulation S-X, Genome
Therapeutics Corp. has obtained a letter of representation from Arthur Andersen
LLP ("Andersen") stating that the December 31, 2001 audit was subject to their
quality control system for the U.S. accounting and auditing practice to provide
reasonable assurance that the engagement was conducted in compliance with
professional standards, that there was appropriate continuity of Andersen
personnel working on the audit and availability of national office
consultation.  Availability of personnel at foreign affiliates of Andersen is
not relevant to this audit.

                               Very truly yours,

                               Genome Therapeutics Corp.

                               /s/ Stephen Cohen

                               Stephen Cohen
                               Senior Vice President and Chief Financial Officer