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Background International data on anogenital HPV infection incidence among men are limited. Methods Incidence of incident-persistent (IP) anogenital HPV infections was evaluated among 295 men who have sex with men (MSM) and 1576 heterosexual men (HM) aged 16–27 years in the placebo arm of a global, multicenter 4-valent (4v) HPV vaccine trial. We estimated IP incidence (penile/scrotal, perineal/perianal, anal) for 4vHPV and 9-valent (9v) HPV vaccine types and cumulative IP incidence over 36 months. Results IP infection incidence per 100 person-years (95% CI) among HM for 4vHPV and 9vHPV types was 4.1 (3.5–4.9) and 6.8 (5.9–7.6) at penile/scrotal, and 1.2 (.8–1.6) and 1.9 (1.5–2.4) at perineal/perianal sites, respectively; and among MSM, IP infection incidence was 2.3 (1.3–3.8) and 3.2 (2.0–4.9) at penile/scrotal, 6.8 (4.9–9.2) and 9.0 (6.9–11.6) at perineal/perianal, and 12.0 (9.4–15.1) and 16.8 (13.7–20.2) at anal sites, respectively. Cumulative IP incidence over 36 months (excluding anal canal; any 9vHPV type) was higher among MSM versus HM (24.1% vs 18.4%). Conclusions A substantial proportion of unvaccinated men of catch-up vaccination age developed IP 9vHPV-related infections. Gender-neutral vaccination could decrease male HPV infection, contribute to herd protection, and reduce disease burden. Clinical Trials Registration. NCT00090285. [ABSTRACT FROM AUTHOR]