The effects of antibiotics used for prophylaxis in women with recurrent urinary tract infections (UTIs) on the aerobic intestinal flora were investigated. Twenty-one patients with recurrent UTIs were randomly divided into three groups. The patients of each group received monotherapy with oral norfloxacin, trimethoprim-sulfamethoxazole or nitrofurantoin for one month. Urine and stool quantitative aerobic cultures were performed before prophylaxis, 2 and 4 weeks after the initiation of therapy, and 2 weeks after antibiotics were discontinued. The gram-negative aerobic flora was strongly suppressed during the administration of norfloxacin and trimethoprim-sulfamethoxazole, while Enterococcus spp. were not affected. Resistant strains of Escherichia coli were detected in two patients, one in the norfloxacin and one in the trimethoprim-sulfamethoxazole group. The aerobic intestinal flora was not affected by nitrofurantoin. These findings help in the selection of the most appropriate antimicrobial agent for prophylaxis in recurrent UTIs, so as to reduce the possibility of emergence of resistant bacterial strains.