BACKGROUND: Screening women for Chlamydia trachomatis in family planning clinics is associated with a reduced incidence of chlamydial sequelae. However, the question of whom to screen to maintain efficient use of resources remains controversial. OBJECTIVE: To assess the cost-effectiveness of chlamydial screening done according to three sets of criteria in asymptomatic women attending family planning clinics. DESIGN: Cost-effectiveness analysis done by using a decision model with the perspective of a health care system. Model estimates were based on analysis of cohort data, clinic costs, laboratory costs, and published data. SETTING: Two family planning clinics in Baltimore, Maryland. PATIENTS: 7699 asymptomatic women who presented between April 1994 and August 1996. INTERVENTION: Three screening strategies--screening according to the criteria of the Centers for Disease Control and Prevention (CDC), screening all women younger than 30 years of age, and universal screening--were retrospectively applied and compared. All women were tested with polymerase chain reaction. MEASUREMENTS: Medical outcomes included sequelae prevented in women, men, and infants. Total costs included screening program costs and future medical costs of all sequelae. The incremental cost-effectiveness ratios of each strategy were calculated. RESULTS: Without screening, 152 cases of pelvic inflammatory disease would occur at a cost of $676,000. Screening done by using the CDC criteria would prevent 64 cases of pelvic inflammatory disease at a cost savings of $231,000. Screening all women younger than 30 years of age would prevent an additional 21 cases of pelvic inflammatory disease and save $74,000. Universal screening would prevent an additional 6 cases of pelvic inflammatory disease but would cost $19,000 more than age-based screening, or approximately $3000 more per case of pelvic inflammatory disease prevented. If the prevalence of C. trachomatis is more than 10.2% or if less than 88.5% of infections occur in women younger than 30 years of age, universal screening provides the greatest cost savings. CONCLUSIONS: These results suggest that age-based screening provides the greatest cost savings of the three strategies examined. However, universal screening is desirable in some situations. In general, screening done by using any criteria and a highly sensitive diagnostic assay should be part of any chlamydial prevention and control program or health plan.