Exhibit 99.11

CONSENT

The undersigned, who has agreed to serve as a member of the Board of Directors of Genome Therapeutics Corp. (the “Company”) following the completion of the merger between Genesoft Pharmaceuticals, Inc. and Guardian Acquisition, Inc., a wholly-owned subsidiary of the Company, hereby grants the Company consent to use his name in its Registration Statement on Form S-4 and all amendments, including post-effective amendments, to the Registration Statement (or any other Registration Statement for the same offering that is to be effective upon filing pursuant to Rule 462(b) under the Securities Act of 1933).

Dated: December 29, 2003

/s/    William J. Rutter                    

        William J. Rutter