The goal of this review is to summarise epidemiological data that support an understanding of the natural history of anal human papillomavirus (HPV) among women and men having sex with women (MSW). HPV is a common infection of the anal canal among women and MSW. Although there have been a limited number of studies to date, both oncogenic and nononcogenic HPV genotypes commonly occur among these populations even when individuals do not report receptive anal sex. Genotype distribution is quite diverse, with recent studies typically detecting more than two dozen genotypes in the anal canal in samples of women and MSW. Factors most consistently associated with HPV in the anal canal among both women and MSW are lifetime number of sexual partners and detection of HPV at the genitals. The common finding of genotypic concordance between the genitals and anal canal in women and MSW, and the infectious nature of HPV, in addition to a limited number of studies offering empirical evidence of anal-to-genital self-inoculation and evidence of HPV hand carriage, may help explain the detection of HPV in the anal canal outside the context of receptive anal sex. HPV vaccination has been shown to reduce anal HPV infection among women and is also a promising prevention strategy among MSW.