Studies on the epidemiology and natural history of anal human papillomavirus (HPV) infection are essential to understand the significance of this virus in the aetiology of anal cancer in men who have sex with men (MSM). This paper presents a review of studies on anal HPV in MSM. For this review, a Medline search was performed to identify English-language articles published in peer-reviewed journals on the epidemiology, natural history and risk factors for anal HPV infection in MSM. Anal HPV prevalence is high in MSM and infection with multiple HPV types is common. The available prospective data suggest detection of new anal HPV infections may also be common. However, with limited epidemiological data available on infection dynamics and associated behavioural risk factors, it is difficult to draw conclusions on how persistent anal HPV infection is in this population.