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Incidence of anal cancer is highest in gay and bisexual men (GBM). A better understanding of the natural history of anal high-risk human papillomavirus (HRHPV) infection is needed for anal cancer prevention. The Study of the Prevention of Anal Cancer was a 3-year study of Australian GBM, aged 35 years or older. We examined incidence, clearance and risk factors for 13 HRHPV types tested for at baseline and 3 annual visits. In 525 men with ≥ 2 visits, 348 (66.3%) acquired ≥ 1 incident HRHPV infection. HPV16 incidence rates were similar, bu