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(1) Background: We conducted a prospective observational cohort study to measure incidence, persistence, and clearance of anal human papillomavirus (HPV) among men who have sex with men (MSM) in China. (2) Methods: MSM were recruited in Guangzhou, Shenzhen and Wuxi, China in 2017. A tablet-based questionnaire was used to collect sociodemographic and behavioral characteristics. An anal brush sample was collected for HPV testing and genotyping. Participants were followed up 12 months after enrolment. (3) Results: A total of 196 participants completed two HPV tests with a median age of 27.3 (interquartile range (IQR) 24.0–32.8) years. Rate of incidence, persistence, and clearance for HPV among MSM were 31.3 (95% confidence interval (CI) 24.7–39.2), 47.9 (36.8–61.3), and 122.5 (104.3–143.0) per 1000 person months (pm), respectively. HPV 16 (4.1/1000 pm) had the highest incidence rate, and HPV 6 (47.4/1000 pm) had the highest persistence rate. Having lower education and engaging in receptive anal intercourse were potential risk factors of HPV incidence. A higher incidence rate was observed among younger MSM. (4) Conclusions: The high incidence and low clearance of anal HPV highlight the necessity of HPV vaccination among MSM. Further studies are needed to clarify the HPV dynamics at multiple anatomical sites and the burden of HPV-related diseases among MSM. [ABSTRACT FROM AUTHOR]