OBJECTIVE To determine the effect of Candida albicans infection and clotrimazole treatment on vaginal microflora. METHODS Studies were conducted using a model simulating the healthy vaginal ecosystem. The model consisted of a mixed culture of Lactobacillus acidophilus, Staphylococcus epidermidis, Prevotella bivia, and group D Streptococcus sp grown in continuous culture in a chemically defined medium. The status of the model was assessed using a mathematical equation that determines the probability a microflora is normal or abnormal. RESULTS Challenge of the model with C albicans was followed within 24 hours by the development of microbial populations representing an abnormal microflora. Treatment of the system with clotrimazole (100 micrograms/mL) resulted in a decrease in C albicans counts to 0 within 48 hours. However, treatment also altered other components of the vaginal microflora, which did not return to normal. Addition of clotrimazole (100 micrograms/mL) to the system in the absence of C albicans also resulted in an abnormal model by 24 hours. CONCLUSIONS Candida albicans infection of the vaginal ecosystem, as represented by this in vitro model, has a deleterious effect on members of the normal microflora. Clotrimazole, although effective against C albicans infection, also has a deleterious effect on components of the normal vaginal microflora. One of the implications for women using clotrimazole for microbiologically undocumented vaginal yeast infections is an increased risk of infection or disease through the disruption of the protective microflora barrier.