The prevalence of asymptomatic chlamydial and gonococcal infections in male and female military populations was determined using urine-based ligase chain reaction DNA amplification assays (DAAs). Cross-sectional surveys in four military settings revealed an overall prevalence of asymptomatic chlamydial infection of 4.2% (56/1338). This included 3.4% (21/618) of Western Pacific shipboard US Marine Corps enlisted men; 5.2% (21/406) of male marines shore-based in Okinawa, Japan; 2.7% (5/183) of female enlisted US Navy subtender personnel in dry dock; and 6.9% (9/131) of shore-based female naval personnel in San Diego. No gonococcal infections were detected. All subjects were treated within 2 weeks of screening; none of them had progressed to symptomatic disease. General population-based screening for asymptomatic sexually transmitted diseases, and in particular chlamydial infection, can be successfully implemented using urine-based DAA tests. Benefits are maximized in a population in which compliance for follow-up therapy is high.