Objectives: The study determined prevalence of asymptomatic nonurethral gonorrhea and chlamydia in men who have sex with men (MSM) seen at the Columbia University Health Service for routine care. Participants: The study enrolled 200 participants from March 2007 to May 2010. Results: Specimens were tested using culture and nucleic acid amplification testing (NAAT): 3.5% (n = 7) tested positive for pharyngeal gonorrhea by NAAT, none were positive by culture; 3% (n = 6) tested positive for rectal chlamydia by NAAT and 0.5% (n = 1) by culture. Conclusions: The incidence of pharyngeal gonorrhea and rectal chlamydia in MSM who visited the Columbia Health Service was similar to rates of asymptomatic nonurethral gonorrhea and chlamydia in studies conducted in the MSM population in non-university settings. This suggests that, following the Centers for Disease Control and Prevention guidelines, 3-site testing for MSM seen at the Columbia clinic is indicated. NAAT is more sensitive than culture for nonurethral gonorrhea and chlamydia.