Study objective: Neisseria gonorrhoeae and Chlamydia trachomatis are the most common bacterial sexually transmitted diseases (STDs) in sexually active youth and many infections are asymptomatic or unrecognized. This study used ligase chain reaction assays for determination of prevalence of gonococcal and chlamydial infections in adolescents seeking care at an urban emergency department. Methods: An unlinked prevalence study was performed with ligase chain reaction tests on voided urine specimens from a convenience sample of adolescents 14 years or older who sought care at the Children's Hospital of Alabama ED. Demographic data and data on care provided in the ED were determined from retrospective chart review of those patients whose urine specimens were tested. Results: Of 282 urine specimens screened, 13.5% (38) yielded positive findings on ligase chain reaction testing for either or both pathogens (20 [7%] positive for N gonorrhoeae, 23 [8%] positive for C trachomatis). In the context of acute care, gonorrhea or chlamydial infection was diagnosed in 5 (1.8%). STD prevalence did not vary significantly by age. Only 39% (15/38) of patients with infections detected by ligase chain reaction testing received potentially effective antibiotics as a result of their urgent care evaluation. Conclusion: Many adolescents use the ED for nonurgent care and unsuspected STDs are often missed. Urine ligase chain reaction testing is a sensitive, noninvasive means of detecting STDs by which unsuspected adolescent STD cases can be detected in an ED setting.