Chlamydia trachomatis infection is common among sexually active populations and often asymptomatic. Infection is associated with complications, including pelvic inflammatory disease and infertility. Using a noninvasive urine ligase chain reaction assay, we determined the prevalence of asymptomatic C. trachomatis infection among sexually active military dependent adolescents and young adults attending clinics at military facilities in San Antonio. The overall prevalence rate was 14%, higher than that reported in many high-risk settings, including sexually transmitted disease clinics. Gender-specific rates were 15% for females and 11% for males. Given a clear cost benefit to screening and treating at-risk populations, we conclude that screening of all sexually active military dependents, both male and female, using this noninvasive test should be performed routinely.