BACKGROUND: Men who have sex with men (MSM) using HIV pre-exposure prophylaxis (PrEP) may be at high risk for bacterial sexually transmitted infections (STIs). We examined the prevalence of extragenital gonorrhea and chlamydia by PrEP status among a multisite sample of US MSM. METHODS: MSM aged ≥18 years were recruited through venue-based sampling to participate in the 2017 National HIV Behavioral Surveillance. In 5 cities (San Francisco, Washington DC, New York City, Miami, and Houston), participants completed a questionnaire, HIV testing, and pharyngeal and rectal STI specimen self-collection. We measured prevalence of pharyngeal and rectal gonorrhea and chlamydia among self-reported non-HIV-positive MSM who reported using or not using PrEP in the previous 12 months. RESULTS: Overall, 29.6% (481/1627) of non-HIV-positive MSM reported PrEP use in the past year. MSM who reported PrEP use were more likely to have any STI (ie, extragenital gonorrhea and/or chlamydia) than MSM not on PrEP [14.6% vs. 12.0%, adjusted prevalence ratio (aPR) = 1.5, 95% confidence interval (CI) : 1.1 to 2.0], reflecting differences in rectal chlamydia prevalence (8.7% vs. 6.0%, aPR = 1.6, 95% CI: 1.1 to 2.4). PrEP use was not associated with pharyngeal chlamydia, pharyngeal gonorrhea, or rectal gonorrhea. CONCLUSIONS: The prevalence of extragenital STI was high for both MSM on PrEP and those not on PrEP in the past year. MSM on PrEP were more likely to have rectal chlamydia but not pharyngeal STIs or rectal gonorrhea. Our findings support regular STI testing at exposed anatomic sites as recommended for sexually active MSM, including those on PrEP.