Most infections after abdominal operations are endogenous and occur by disseminating bacteria present in the intestinal tract during operation. The risk of developing surgical site infection after abdominal operations is related to the extent of intestinal contamination during operation and to the density and type of bacteria in the intestinal tract. Although antimicrobial prophylactic agents must be active against contaminating bacteria during operation, it should not cover all contaminating bacteria but Staphylococcus aureus except MRSA, Escherichia coli, Klebsiella spp., Enterobacter spp., Citrobacter spp., Proteus spp. and Bacteroides spp. As the isolation rate and type of bacteria from primary abdominal infections such as perforated peritonitis and biliary tract infection are resemble to those of bacteria contaminating during operations, antimicrobial prophylactic agents could be chosen considering activities against bacteria isolated from primary infections. According to the isolation rates of these bacteria and antibiotic susceptibilities, cefotiam (CTM) is considered to have most strong activities as prophylactic agent for abdominal surgery, followed by cefmetazole (CMZ) and cefazolin (CEZ), in this order. In order to establish the fundamental principle of antimicrobial prophylaxis in surgery, these results should be evaluated by clinical prospective randomized studies in the near feature.