BACKGROUND: Sexually transmitted diseases (STD) are frequently asymptomatic and increase the likelihood of transmitting and acquiring HIV. In Brazil, the guidelines for STDs diagnosis and treatment are based on the syndromic approach. Nucleic acid amplification tests (NAAT) has been recommended as routine STDs screening in some countries, especially for men who have sex with men (MSM). Limited data are available about how to best define target groups for routine screening by NAATs within this population. We aimed to assess the prevalence of rectal and urethral Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) infections and syphilis, and the factors associated with having at least one STD among HIV-infected and uninfected MSM in Rio de Janeiro, Brazil. METHODS: From August 2010 to June 2012, 391 MSM were enrolled into the Evandro Chagas National Institute of Infectious Diseases-INI-Fiocruz cohort, and 292 MSM (HIV-infected:211 and HIV-uninfected:81) were included in this study. NAATs were performed on the rectal swabs and urine for CT and NG. The rapid plasma reagin test and microhemagglutination assay for Treponema pallidum were performed for syphilis diagnosis. RESULTS: The overall prevalence of STD was 20.0% (95%CI:15.7-25.1): 10% anorectal chlamydia; syphilis 9.9%; anorectal gonorrheae 2.5%; and urethral chlamydia 2.2%; no case of urethral gonorrheae was detected. The proportion of HIV-positive MSM who had at least one STD was nearly two times that of HIV-negative MSM (22.6% vs 13.2%; P = 0.09). The frequency of each STD, except for anorectal NG (1.5% vs.5.2%), was higher among HIV-positive than HIV-negative individuals. Among the 211 asymptomatic participants, 17.5% (n = 37) were identified as having at least one STD; 10.4% (n = 22/211) tested positive for anorectal chlamydia. Sixty five percent of HIV-positive MSM were asymptomatic at the time of the STD diagnosis, while 100.0% of the HIV-negative MSM. Age (APR = 0.78; 95%CI:0.60-1.00 for each additional ten years) and a positive-HIV serostatus (APR = 2.05; 95%CI:1.03-4.08) were significantly associated with STD diagnosis. CONCLUSION: An overall high STD-prevalence rate was observed, especially among HIV-infected and in younger individuals, and the majority of STDs were asymptomatic. STD screening using NAATs among asymptomatic MSM is a potentially cost-effective intervention for the prevention of HIV infection among MSM.