OBJECTIVE:: The objective of the study was to assess the incidence of, and risk factors for, abnormal anal cytology and anal intraepithelial neoplasia (AIN) 2–3 in human immunodeficiency virus (HIV)–infected women. STUDY DESIGN:: This prospective study assessed 100 HIV-infected women with anal and cervical specimens for cytology and high-risk human papillomavirus (HPV) testing over 3 semiannual visits. RESULTS:: Thirty-three women were diagnosed with an anal cytologic abnormality at least once. Anal cytology abnormality was associated with current CD4 count less than 200 cells/mm, anal HPV infection, and a history of other sexually transmitted infections (STIs). Twelve subjects were diagnosed with AIN2–3: 4 after AIN1 diagnosis and 4 after 1 or more negative anal cytology. AIN2–3 trended toward an association with history of cervical cytologic abnormality and history of STI. CONCLUSION:: Repeated annual anal cytology screening for HIV-infected women, particularly for those with increased immunosuppression, anal and/or cervical HPV, a history of other STIs, or abnormal cervical cytology, will increase the likelihood of detecting AIN2–3.