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PurposeThe aims of this study were to determine prevalence of and factors associated with any human papillomavirus (HPV) and vaccine-type HPV among young men after vaccine introduction, stratified by vaccination status.MethodsYoung men were recruited from clinical sites from 2013 to 2015, completed a survey, and were tested for 36 anogenital HPV types. We determined factors associated with ≥1 HPV type among all participants, and vaccine-type HPV (HPV6, 11, 16, and/or 18) among all, vaccinated and unvaccinated participants, using multivariable regression.ResultsMean age was 21.5 years and 26% had received at least one HPV vaccine dose. HPV prevalence was lower in vaccinated versus unvaccinated young men (50.5% vs. 62.6%, p = .03). HPV positivity was discordant by anogenital site. At both sites, 59.4% were positive for ≥1 HPV type and 26.0% for ≥1 4-valent vaccine type. In multivariable logistic regression, factors associated with ≥1 HPV type among all participants were frequency of oral sex (odds ratio [OR] = 1.80, 95% confidence interval [CI] = 1.00-3.24), recent smoking (OR = 1.84, CI = 1.17-2.90), and sexually transmitted infection history (OR = 1.56, CI = 1.02-2.38). Factors associated with vaccine-type HPV among all participants were white versus black race (OR = 1.91, CI = 1.10-3.34) and gonorrhea history (OR = 2.52, CI = 1.45-4.38); among vaccinated participants were private versus Medicaid insurance (OR = 5.6, CI = 1.46-20.4) and private versus no insurance (OR = 15.9, CI = 3.06-83.3); and among unvaccinated participants was gonorrhea history (OR = 1.83, CI = 1.03-3.24).ConclusionsAnogenital HPV prevalence was high and vaccination rates low among young men 2-4 years after vaccine introduction, underscoring the urgency of increasing vaccination rates and vaccinating according to national guidelines.