Background Gonorrhea (Neisseria gonorrhoeae [GC]) and chlamydia (Chlamydia trachomatis [CT]) disproportionately affect men who have sex with men (MSM), and public health implications vary by anatomic site and bacterial agent. Urethral and rectal GC and CT can increase risk of HIV transmission, whereas pharyngeal GC may be a reservoir for antimicrobial resistance. To define screening priorities in Latin America, we compare differences in the prevalence and correlates of urethral, pharyngeal, and rectal GC and CT among MSM in Peru. Methods A cross-sectional sample of 787 MSM from Lima was screened between 2012 and 2014. We described prevalence of urethral, pharyngeal, and rectal GC and CT infection and conducted bivariate analyses of associations with social, behavioral, and biological characteristics. Poisson regression analyses assessed the correlates of each infection at each anatomic site. Results The most commonly symptomatic infection (urethral GC; 42.1%) was the least prevalent (2.4%). The most prevalent infections were rectal CT (15.8%) and pharyngeal GC (9.9%). Rectal CT was the least commonly symptomatic (2.4%) infection, and was associated with younger age (adjusted prevalence ratio [95% confidence interval], 0.96 [0.94-0.98]), HIV infection (1.46 [1.06-2.02]), and pasivo (receptive; 3.59 [1.62-7.95]) and moderno (versatile; 2.63 [1.23-5.60]) sexual roles. Conclusions Results highlight limitations of current syndromic screening strategies for sexually transmitted diseases in Peru, wherein urethral CT and rectal GC and CT may be missed due to their frequently asymptomatic presentations. Successful management of GC and CT infections among MSM in low-resource settings requires differentiating between bacterial agent, symptomatic presentation, associated risk factors, and public health implications of untreated infection at different anatomic sites.