Objectives: To determine the utility of urine-based ligase chain reaction assays for Neisseria gonorrhoeae and Chlamydia trachomatis in (1) the acceptability of such testing to adolescent detainees, (2) the potential use of these tests for identifying asymptomatic infections, and (3) the effectiveness of this approach for ensuring treatment of infected adolescents. Design: Cross-sectional screening and verification of treatment for infected cases. Subjects: Adolescents admitted to a short-term juvenile detention center. Main Outcome Measures: Neisseria gonorrhoeae and C trachomatis infection rates, and timing and location of treatment for infected patients. Results: Refusal rate was 1.5%. Of 263 participants, 46 (17.5%) were female subjects. Chlamydia trachomatis infections were identified in 28.3% of the female and 8.8% of the male subjects. Neisseria gonorrhoeae infections were present in 13.1% of the female and 2.8% of the male subjects. Overall, 37 participants (14%) were positive for N gonorrhoeae, C trachomatis, or both, only one of whom had symptoms. Almost 70% (25/36) of asymptomatic infected subjects were treated within 28 days of screening. A treatment was documented in 36 of the 37 infected youth, including 20 who were followed up and treated after release from the detention center, by 6 months after testing. Conclusion: Urine ligase chain reaction tests were effective for identifying and guiding treatment of unsuspected N gonorrhoeae and C trachomatis infections in teenagers admitted to a short-term detention center where traditional swab specimens may be difficult to obtain.