A prospective evaluation of 331 university women who were initiating use of oral contraceptive pills (OCPs), a cervical cap, diaphragm-spermicide, or other spermicidal methods was done to assess the effects of commonly used contraceptive methods on the vaginal flora. Vaginal introital cultures were performed at baseline and then weekly for 1 month. The prevalence of Escherichia coli vaginal colonization and of abnormal vaginal Gram stain scores (Nugent criteria) increased significantly among women using a cervical cap or diaphragm-spermicide but not among women using OCPs. Women with E. coli colonization were significantly more likely to have an abnormal Nugent score and an absence of lactobacilli. In a multivariate model, use of spermicidal contraception in the preceding week was associated with an abnormal Nugent score and with colonization with E. coli, Enterococcus species, and anaerobic gram-negative rods. Thus, spermicidal methods of contraception are associated with alterations of the vaginal microflora that consequently may predispose women to genitourinary infections.