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The purpose of this project was to determine the prevalence of asymptomatic sexually transmitted diseases (STDs) among men who have sex with men (MSM) in the Boston area who had been sexually active (oral and/or anal sex) with another male within the past year.Over a 1-month period (March 2007), asymptomatic MSM in care at a Boston community health center (n = 114) were screened for gonorrhea and chlamydia using the BD ProbeTec technique. Deidentified medical record data were analyzed and linked to prevalence monitoring results.Eleven percent of the sample tested positive for one of the 2 STDs (gonorrhea or chlamydia) from at least one mucosal site. Individuals who were infected with an STD were considerably more likely to have a prior history of one or more STD infections when compared with those without an STD history (OR = 3.69; P <0.02). There were no significant differences observed in psychosocial and other behavioral risk factors between patients with or without an STD.Screening asymptomatic MSM using nucleic acid amplification tests (NAATs) revealed a substantial STD burden that might not have been diagnosed using traditional assays. These data are critical for the design of effective public health interventions for this population.