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Context The prevalence and distribution of gonococcal and chlamydial infections in the general population are poorly understood. Development of nucleic acid amplification tests, such as the ligase chain reaction assay, provides new opportunities to estimate the prevalence of untreated infections in the population. Objective To estimate the overall prevalence of untreated gonococcal and chlamydial infections and to describe patterns of infection within specific demographic subgroups of the young adult population in Baltimore, Md. Design and Setting Cross-sectional behavioral survey based on a probability sample of Baltimore households with collection of urine specimens between January 1997 and September 1998. Participants A total of 728 adults aged 18 to 35 years completed the interview portion of the study, and 579 of these respondents also provided a urine specimen adequate for testing. Main Outcome Measure Prevalence of untreated infection, as measured by the percentage of specimens testing positive for gonococcal and chlamydial infection by ligase chain reaction, weighted to reflect variations in probabilities of sample selection from the population. Alternate estimates of the prevalence of recent treated infection were derived from clinically diagnosed cases reported to the Baltimore City Health Department and by diagnoses reported by participants in the survey. Results An estimated 5.3% (SE, 1.4%) of the population aged 18 to 35 years has an untreated gonococcal infection, and 3.0% (SE, 0.8%) is estimated to have an untreated chlamydial infection. While 7.9% (SE, 1.6%) of the population is estimated to have either an untreated gonococcal or chlamydial infection, estimated prevalence is substantially higher among black women (15.0%; SE, 3.7%). Few participants with untreated infections reported dysuria or discharge during the 6 months preceding testing. The estimated number of untreated gonococcal infections in the population (9241; SE, 2441) substantially exceeds both the number of such infections diagnosed among Baltimore adults aged 18 to 35 years and reported to the Baltimore City Health Department during 1998 (4566), and the estimated number of diagnoses derived using participants' reports for the 12 months prior to the survey (4708 [SE, 1918] to 5231 [SE, 2092]). The estimated number of untreated chlamydial infections (5231; SE, 1395) is also greater than the number of cases reported to the health department in 1998 (3664) but is slightly less than the estimated number of diagnoses derived using participants' reports of chlamydial infections diagnosed during the 12 months prior to the survey (5580 [SE, 1918] to 6975 [SE, 2441]). Conclusion In 1997-1998, the estimated number of undiagnosed gonococcal and chlamydial infections prevalent in the population of Baltimore adults aged 18 to 35 years approached or exceeded the number of infections that were diagnosed and treated annually.