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A quadrivalent vaccine that prevents genital warts (GWs) has been recommended by the Advisory Committee on Immunization Practices for women since 2007 and for men since 2011. National estimates of GW burden in sexually transmitted disease (STD) clinic settings are useful to provide a baseline assessment to monitor and evaluate reductions in GW and serve as an important early measure of human papillomavirus (HPV) vaccine impact in this population.Genital wart prevalence among STD clinic patients from January 2010 to December 2011 was determined from a cross-sectional analysis of all patients attending STD clinics in the STD Surveillance Network (SSuN). We conducted bivariate analyses for women, men who have sex with women (MSW), and men who have sex with men (MSM) separately, using χ2 statistics for the association between GW diagnosis and demographic, behavioral, and clinical characteristics.Among 241,630 STD clinic patients, 13,063 (5.4%) had GWs. Wide regional differences were observed across SSuN sites. The prevalence of GW was as follows: 7.5% among MSW (range by SSuN site, 3.9–15.2), 7.5% among MSM (range, 3.3–20.6), and 2.4% among women (range, 1.2–5.4). The highest rate was among 25- to 29-year-old MSW (9.8%). Non-Hispanic black women and MSW had a lower prevalence of GWs than did women and MSW in other racial/ethnic groups.There is a significant burden of GW in STD clinic populations, most notably in men. Given the opportunity for prevention with a quadrivalent HPV vaccine, STD clinics may be an ideal setting for monitoring trends in GW prevalence among men (MSW and MSM). However, given the observed low GW prevalence among female STD clinic patients, STD clinics may not provide an appropriate setting to monitor the impact of HPV vaccine among women.