The effectiveness of selective screening for control of Chlamydia trachomatis is unknown. In 1986, a statewide screening program began in family planning clinics in Wisconsin after the prevalence of infection among women was found to be 10.7% in four nonurban clinics and 13.7% in an urban Milwaukee clinic. In 1990, endocervical specimens were obtained from 1,757 women attending these same clinics; 5.2% of women in the non-urban clinics and 6.9% in the Milwaukee clinic tested positive for C. trachomatis. Prevalence of infection had decreased similarly (by 53% overall) in both high- and low-risk groups in all five clinics. Although reported condom use increased from 16% to 31%, most other demographic and behavioral risk factors for infection did not significantly change; in contrast, the prevalence of clinical signs of infection decreased. The percentage of infections identified by selective screening criteria decreased from 77% to 55%. Selective screening and attendant activities, as well as an increase in condom use, were associated with a decrease in prevalence of C. trachomatis infection in this population.