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Background: Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) infection are prevalent among men who have sex with men (MSM) and may infect multiple anatomic sites. We measured site-specific prevalence and correlates of CT and NG infection among Bangkok MSM Cohort Study participants., Methods: In April 2006 to November 2010, 1744 men enrolled in the Bangkok MSM Cohort Study. Participants provided historical information and underwent physical examination. Rectal, urethral, and pharyngeal CT and NG screening were performed by nucleic acid amplification and/or culture. Logistic regression was used to identify correlates of site-specific CT, NG, and coinfection., Results: Among 1743 participants, 19.2% were infected with CT and/or NG. CT, NG, and CT-NG coinfection were detected in 11.6%, 4.6%, and 2.9%, of participants, respectively. Rectal, urethral, and pharyngeal CT infections were detected in 9.5%, 4.5%, and 3.6% of cases. N. gonorrhoeae was present at these sites in 6.1%, 1.8%, and 0.5% of cases. Most infections were asymptomatic (CT: 95.3%, NG: 83.2%). Rectal CT and NG infections were mutually associated (CT: adjusted odds ratio [AOR], 5.4; 95% confidence interval [CI], 3.4-8.7; NG: AOR, 2.4; 95% CI, 1.1-5.2) and independently associated with HIV infection (CT: AOR, 1.6, 95% CI, 1.0-2.4; NG: AOR, 2.0, 95% CI, 1.3-3.1). Numerous behavioral correlates of infection were observed., Conclusions: CT and NG infections are highly prevalent among MSM in Bangkok, most frequently affect the rectum, and are most often asymptomatic. Routine screening of asymptomatic MSM for CT and NG infection should include rectal sampling and focus on men with HIV and a history of other sexually transmitted infections.