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Few data are available on the prevalence of sexually transmitted diseases (STDs) in men who have sex with men (MSM), making it difficult to develop STD screening guidelines for this population. The objective of the study was to determine the prevalence of urethral infections caused by Chlamydia trachomatis and Neisseria gonorrhoeae within a large, community based population of MSM, and to assess the feasibility of rectal screening in this population.This was a cross sectional study of 566 MSM, who were predominantly middle aged, white, asymptomatic, and engaged in sex with multiple partners. All provided a urine sample to screen for chlamydial and gonorrhoea infections using a PCR assay; rectal screening was performed on 48 participants.Urethral C trachomatis infections were detected in 1/566 participants (prevalence 0.2%, 95% CI 0.004% to 1.0%), and rectal C trachomatis infections were detected in 2/48 men (prevalence 4.2%, 95% CI 0.5% to 14.2%). No gonorrhoea infections were detected, and none of the 117 HIV positive men had either infection.Chlamydial and gonorrhoea infections were uncommon in this sample of MSM, even among those with multiple sexual partners or HIV infection. These data call into question recommendations to screen all MSM based on their individual sexual behaviours or HIV. Additional data are needed on the prevalence of these infections in MSM from different settings.