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OBJECTIVES: A large portion of anogenital cancers is caused by high-risk human papillomavirus (hrHPV) infections, which are especially common in HIV-infected men. We aimed to compare the incidence and clearance of anal and penile hrHPV infection between HIV-infected and HIV-negative MSM. DESIGN: Analyses of longitudinal data from a prospective cohort study. METHODS: MSM aged 18 years or older were recruited in Amsterdam, the Netherlands, and followed-up semi-annually for 24 months. At each visit, participants completed risk-factor questionnaires. Anal and penile self-samples were tested for HPV DNA using the SPF10-PCR DEIA/LiPA25 system. Effects on incidence and clearance rates were quantified via Poisson regression, using generalized estimating equations to correct for multiple hrHPV types. RESULTS: Seven hundred and fifty MSM with a median age of 40 years (interquartile 35-48) were included in the analyses, of whom 302 (40%) were HIV-infected. The incidence rates of hrHPV were significantly higher in HIV-infected compared with HIV-negative MSM [adjusted incidence rate ratio (aIRR) 1.6; 95% confidence interval (CI) 1.3-2.1 for anal and aIRR 1.4; 95%CI 1.0-2.1 for penile infection]. The clearance rate of hrHPV was significantly lower for anal [adjusted clearance rate ratio (aCRR) 0.7; 95%CI 0.6-0.9], but not for penile infection (aCRR 1.3; 95%CI 1.0-1.7). HrHPV incidence or clearance did not differ significantly by nadir CD4 cell count. CONCLUSION: Increased anal and penile hrHPV incidence rates and decreased anal hrHPV clearance rates were found in HIV-infected compared with HIV-negative MSM, after adjusting for sexual behavior. Our findings suggest an independent effect of HIV infection on anal hrHPV infections.