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Background: Current guidelines recommend screening for extragenital gonorrhea (GC) and chlamydia (CT) only among men having sex with men (MSM). Extragenital GC and CT is associated with treatment failure and disease transmission. The prevalence of extragenital GC/CT infections in women and in men having sex with women (MSW) are less well studied. We sought to determine the prevalence of extragenital CG and CT among all persons attending a sexually transmitted diseases clinic who engaged in extragenital sexual activity., Methods: We examined demographic and clinical data of all patients who engaged in extragenital sexual activity between January 2012 and October 2014. Nucleic acid amplification testing for GC and CT was performed at sites of exposure among all men and women at pharyngeal, rectal, and urogenital sites. Multivariable logistic regression analyses were performed to determine the extent that age, race/ethnicity, and number of sexual partners predicted a positive test result., Results: Pharyngeal GC was found in 3.1% of MSW, representing 35% of the GC infections in MSW. Thirty-six percent of MSW with pharyngeal GC tested negative at their urogenital site. Pharyngeal GC in MSW prevalence was higher among those with younger age or a higher number of sex partners. Pharyngeal GC, rectal GC, and rectal CT rates were 8.5%, 15.0%, and 16.5%, respectively, among MSM and 3.8%, 4.8%, and 11.8% among women having sex with men (WSM), respectively., Conclusions: Extragenital GC and CT rates of infection was highest among MSM but was also observed in WSM and MSW, representing an unrecognized disease burden.