OBJECTIVE To determine the prevalence of anal human papillomavirus (HPV) infections and anal cytologic abnormalities in HIV-seropositive and HIV-seronegative women. METHODS This cross-sectional study of a cohort of women with known HIV serostatus involved a standardized interview and a gynecologic examination, including a cytologic evaluation of the cervix and anus. Anal swabs were tested for HPV DNA using the Hybrid Capture assay. METHODS Two HIV/AIDS clinics, a sexually transmitted disease clinic, a methadone clinic and women enrolled in a study of HIV heterosexual transmission in the greater New York City metropolitan area. METHODS One hundred and two HIV-seropositive and 96 HIV-seronegative women were selected from an ongoing study of the gynecologic manifestations of HIV infection. METHODS Detection of anal HPV DNA and anal cytologic abnormalities. RESULTS Anal cytologic abnormalities were detected in 27 (26%) of the 102 HIV-seropositive women and in six (7%) of 96 HIV-seronegative women. Five (5%) of the anal smears from the HIV-seropositive women and one (1%) from the HIV-seronegative women had low-grade anal intra-epithelial neoplasia. The remainder of the anal cytologic abnormalities were classified as mild squamous cytologic atypia. HPV DNA was detected in 30 (29%) of 102 HIV-seropositive and two (2%) of 96 HIV-seronegative women. Of the 33 patients with anal cytologic abnormalities, 19 (58%) had anal HPV DNA detected as compared to 13 (8%) of 160 women without cytologic abnormalities (P < 0.001). In a multivariate logistic regression analysis, HIV-seropositivity was found to be an independent risk factor for both anal HPV infection and anal cytologic abnormalities and the strength of the association was greater in women with lower CD4+ T-lymphocyte counts. CONCLUSIONS The prevalence of both anal cytologic abnormalities and anal HPV infection are significantly increased in HIV-seropositive women.