OBJECTIVE: To determine utility of a polymerase chain reaction (PCR) based urine screening for C. trachomatis (CT) in health care of females in an urban adolescent clinic. METHOD: Study design was a cross-sectional screening of non-sterile, random samples of urine with a PCR-based lab test for CT (PCR-CT). In an independent study of 251 females, the PPV and NPV of the urine PCR-CT in our STD Research Lab were 94% and 96% respectively, compared with the tissue culture of endocervical swabs. The study setting was Adolescent Clinic in an urban Children's Hosp. Inclusion criteria were females ≥15 years of age, on no antibiotics and a verbal consent to participate. Each eligible subject attending the target clinic between 3/95 and 8/95 was approached consecutively with an explanation of the study. Reason(s) for the index visit, past history of CT, gonorrhea (GC) and PID, and genitourinary/ abdominal (GU) complaints were obtained from each subject. An endocervical CT culture was done during the index visit, if the subject had a clinical indication for pelvic exam. RESULTS: 208 subjects (73% B, 27% W; mean age 17 yrs) were enrolled. Primary reason for the visit was family planning in 41%, check-up in 29%, contact with STD in 2% and a wide range of other complaints in the rest. A GU complaint was present in 26%. Reported Hx of STDs were: CT in 15%, GC in 9% and PID in 7%. 33% including a majority with the GU complaints had a CT culture during the index visit. A positive urine PCR-CT was identified in 34 (16.4%); 11 of those were also identified by a CT culture of endocervical swabs; the remaining 23 were not among those who had a pelvic examination. All PCR-CT positive subjects were treated. Family planning visit was the only predictor for pos PCR-CT (p=.05). GU symptoms did not correlate with a pos test. CONCLUSION: Utility of PCR-based urine screening for CT in care of adolescent females is demonstrated. A urine specimen is easy to collect and the result of PCR-CT, if batched and performed daily, is available within 24 hours, in contrast to 48-72 hours for the culture. Without PCR-CT, 2/3 of CT infected cases in the study would have been undiagnosed.