Objective The aim of this study was to systematically review the findings of publications addressing the epidemiology of anal HPV infection, anal intraepithelial neoplasia and anal cancer in women. Data Sources We conducted a systematic review among publications published from January 1, 1997 to September 30, 2013 in order to limit to publications from the combined antiretroviral therapy (cART) era. Three searches were performed of the National Library of Medicine PubMed database using the following search terms: “women and anal HPV”, “women anal intraepithelial neoplasia”, and “women and anal cancer.” Study Eligibility Criteria Publications were included in the review if they addressed any of the following outcomes: (1) prevalence, incidence, or clearance of anal HPV infection, (2) prevalence of anal cytological or histological neoplastic abnormalities, or (3) incidence or risk of anal cancer. Thirty-seven publications addressing anal HPV infection and anal cytology remained after applying selection criteria, and 23 anal cancer publications met the selection criteria. Results Among HIV-positive women, prevalence of HR-HPV in the anus was 16-85%. Among HIV-negative women, prevalence of anal HR-HPV infection ranged from 4 - 86%. The prevalence of anal HR- HPV in HIV-negative women with HPV-related pathology of the vulva, vagina and cervix compared with women with no known HPV-related pathology, varied from 23-86%, and 5-22%, respectively. Histologic anal HSIL (AIN 2+) was found in 3-26% of the women living with HIV, 0-9% among women with lower genital tract pathology, and 0-3% for women who are HIV-negative without known lower genital tract pathology. The incidence of anal cancer among HIV-infected women ranged from 3.9-30 per 100,000. Among women with a history of cervical cancer or CIN 3, the IR of anal cancer ranged from 0.8-63.8/100,000 person-years, and in the general population, the IRs ranged from 0.55-2.4/100,000 person-years. Conclusions This review provides evidence that anal HPV infection and dysplasia are common in women, especially in those who are HIV-positive or have a history of HPV-related lower genital tract pathology. The incidence of anal cancer continues to grow in all women, especially those living with HIV, despite the widespread use of cART.