BACKGROUND: We evaluated the cost-effectiveness of Chlamydia screening strategies that use different methods of specimen collection: cervical swabs, urines, and self-obtained vaginal swabs. METHODS: A decision analysis was modeled for a hypothetical cohort of 10,000 per year of women attending sexually transmitted disease (STD) clinics. Incremental cost-effectiveness of 4 screening strategies were compared: 1) Endocervical DNA probe test (PACE2, Gen-Probe), 2) Endocervical AC2 (Aptima Combo 2, Gen-Probe), 3) Self-Obtained Vaginal AC2, and 4) Urine AC2. Sensitivities of the vaginal, urine, and cervical AC2 tests were derived from 324 women attending STD clinics. The primary outcome was cases of pelvic inflammatory disease prevented. The model incorporated programmatic screening and treatment costs and medical cost savings from sequelae prevented. RESULTS: Chlamydia prevalence in the sampled population was 11.1%. Sensitivities of vaginal, urine, and cervical AC2 were 97.2%, 91.7%, and 91.7%, respectively. The sensitivity of the DNA probe was derived from the literature and estimated at 68.8%. The self-obtained vaginal AC2 strategy was the least expensive and the most cost-effective, preventing 17 more cases of pelvic inflammatory disease than the next least expensive strategy. CONCLUSIONS: Use of a vaginal swab to detect Chlamydia in this STD clinic population was cost-saving and cost-effective.