1 EXHIBIT 11.1 GENOME THERAPEUTICS CORP. AND SUBSIDIARIES CALCULATION OF SHARES USED IN DETERMINING PRIMARY NET INCOME (LOSS) PER SHARE YEAR ENDED AUGUST 31, 1994 1995 1996 ------------------------------------- Weighted average common stock outstanding during the year 11,097,224 12,287,918 15,530,639 Weighted average common stock equivalents outstanding during the year -- 673,816 2,599,155 ------------------------------------- 11,097,224 12,961,734 18,129,794 ===================================== CALCULATION OF SHARES USED IN DETERMINING FULLY DILUTED NET INCOME (LOSS) PER SHARE YEAR ENDED AUGUST 31, 1994 1995 1996 ------------------------------------- Weighted average common stock outstanding during the year 11,097,224 12,287,918 15,530,639 Weighted average common stock equivalents outstanding during the year -- 748,823 2,599,155 ------------------------------------- 11,097,224 13,036,741 18,129,794 =====================================