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Although a potentially important route for transmission, limited data exist on the burden of pharyngeal chlamydia (CT) and gonorrhea (GC) among men who have sex with men (MSM). We examined pharyngeal CT and GC among MSM screened in San Francisco in 2010.MSM seeking services in a variety of clinical settings provided clinician-collected pharyngeal specimens that were tested using the APTIMA Combo 2 platform. The prevalence of pharyngeal CT and GC was estimated at 5 sentinel sites: the municipal STD clinic, a gay men's health clinic, an HIV care clinic, an HIV testing site, and primary care clinics supported by the San Francisco Department of Public Health. Positivity for each infection was calculated as the number of positive tests divided by the number of testers with corresponding confidence intervals (CI).In 2010, a total of 12,454 pharyngeal CT specimens and 12,457 pharyngeal GC specimens were tested for an overall CT positivity of 1.69% (95% CI: 1.47–1.93) and GC positivity of 5.76% (95% CI: 5.36–6.19). At the 5 sentinel sites, pharyngeal CT positivity ranged from 1.10% (HIV testing site) to 2.28% (STD clinic); pharyngeal GC positivity ranged from 3.4% (HIV testing site) to 7.01% (STD clinic).Sentinel surveillance data indicate that there is a substantial burden of pharyngeal CT and GC infections among MSM in San Francisco. Identification and treatment of pharyngeal infections could prevent ongoing transmission of these bacteria. Increasing access to nucleic acid amplification tests-based pharyngeal screening should be a public health priority.