BACKGROUND: The Centers for Disease Control and Prevention recommends pharyngeal screening of Neisseria gonorrhoeae (GC) and rectal screening of GC and Chlamydia trachomatis (CT) in HIV-infected and at-risk men who have sex with men (MSM). There are currently no recommendations to routinely screen women at extragenital sites. We define the prevalence of extragenital GC and CT in women attending 2 urban sexually transmitted disease clinics in Baltimore City and compare it with the prevalence of extragenital infections in MSM and men who have sex with women. METHODS: All patients who reported extragenital exposures in the preceding 3 months, who presented for care between June 1, 2011, and May 31, 2013, and who were tested for GC and CT using nucleic acid amplification tests at all sites of exposure were included in the analyses. We used logistic regression models to identify risk factors for extragenital infections. RESULTS: A total of 10,389 patients were included in this analysis (88% African American; mean age, 29 years; 42% women; 7% MSM; 2.5% HIV infected). The prevalence estimates of any extragenital GC and CT were as follows: 2.4% GC and 3.7% CT in women, 2.6% GC and 1.6% CT in men who have sex with women, and 18.9% GC and 11.8% CT in MSM. Among women, 30.3% of GC infections and 13.8% of CT infections would have been missed with urogenital-only testing. Unlike MSM, age ≤ 18 years was the strongest predictor of extragenital infections in women. CONCLUSIONS: Although the prevalence of extragenital gonorrhea and chlamydia is highest in MSM, a significant number of GC and CT infections in young women would be missed with genital-only testing. Cost-effectiveness analyses are needed to help inform national guidelines on extragenital screening in young women.