Exhibit 99.2 CERTIFICATION PURSUANT TO SECTION 1350, CHAPTER 63 OF TITLE 18, UNITED STATES CODE, AS ADOPTED PURSUANT TO SECTION 906 OF THE SARBANES-OXLET 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 Senior Vice President and Chief Financial 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/ Stephen Cohen ------------------------- Stephen Cohen Senior Vice President & Chief Financial Officer Dated: November 12, 2002