Exhibit 99.1

                            CERTIFICATION PURSUANT TO
            SECTION 1350, CHAPTER 63 OF TITLE 18, UNITED STATES CODE,
                             AS ADOPTED PURSUANT TO
                  SECTION 906 OF THE SARBANES-OXLEY ACT OF 2002

Pursuant to Section 1350, Chapter 63 of Title 18, United States Code, as adopted
pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, the undersigned, as
President and Chief Executive Officer of Genome Therapeutics Corp. (the
"Company") does hereby certify that to my knowledge:

             1)   the Company's Report on Form 10-Q for the quarter ended
                  September 28, 2002, fully complies with the requirements of
                  Section 13(a) or 15(d) of the Securities Exchange Act of 1934;
                  and

             2)   the information contained in the Company's Report on Form 10-Q
                  for the quarter ended September 28, 2002, fairly presents, in
                  all material respects, the financial condition and results of
                  operations of the Company.

         By:          /s/ Steven M. Rauscher
                      --------------------------------
                      Steven M. Rauscher
                      President & Chief Executive Officer

                      Dated:  November 12, 2002