Background: Men who have sex with men (MSM) are at greatly increased risk of human papillomavirus (HPV)-associated anal cancer. Screening for the presumed cancer precursor, high-grade anal intraepithelial neoplasia (AIN), followed by treatment in a manner analogous to cervical screening, has been proposed. We aimed to assess available data for anal HPV disease that can inform pre-cancer screening programmes. Methods: We searched PubMed, OVID Medline, and Embase for all studies published before Nov 1, 2011, that reported prevalence and incidence of anal HPV detection, AIN, and anal cancer in MSM. We calculated summary estimates using random-effects meta-analysis. Findings: 53 studies met the inclusion criteria, including 31 estimates of HPV prevalence, 19 estimates of cytological abnormalities, eight estimates of histological abnormalities, and nine estimates of anal cancer incidence. Data for incident HPV and high-grade AIN were scarce. In HIV-positive men, the pooled prevalence of anal HPV-16 was 35·4% (95% CI 32·9-37·9). In the only published estimate, incidence of anal HPV-16 was 13·0% (9·6-17·6), and clearance occurred in 14·6% (10·2-21·2) of men per year. The pooled prevalence of histological high-grade AIN was 29·1% (22·8-35·4) with incidences of 8·5% (6·9-10·4) and 15·4% (11·8-19·8) per year in two estimates. The pooled anal cancer incidence was 45·9 per 100 000 men (31·2-60·3). In HIV-negative men, the pooled prevalence of anal HPV-16 was 12·5% (9·8-15·4). Incidence of HPV-16 was 11·8% (9·2-14·9) and 5·8% (1·9-13·5) of men per year in two estimates. The pooled prevalence of histological high-grade AIN was 21·5% (13·7-29·3), with incidence of 3·3% (2·2-4·7) and 6·0% (4·2-8·1) per year in two estimates. Anal cancer incidence was 5·1 per 100 000 men (0-11·5; based on two estimates). There were no published estimates of high-grade AIN regression. Interpretation: Anal HPV and anal cancer precursors were very common in MSM. However, on the basis of restricted data, rates of progression to cancer seem to be substantially lower than they are for cervical pre-cancerous lesions. Large, good-quality prospective studies are needed to inform the development of anal cancer screening guidelines for MSM. Funding: Australian Government Department of Health and Ageing.