Identifying factors, including human papillomavirus (HPV) genotypes, associated with abnormal anal cytology in HIV-infected women have implications for anal squamous cell cancer (SCC) prevention in HIV-infected women. Anal and cervical samples were collected for cytology, and tested for high-(HR-HPV) and low-risk HPV (LR-HPV) genotypes in a cross-sectional analysis of the IPEC Women's HIV Cohort (Rio de Janeiro, Brazil). Multivariate log-binomial regression models estimated prevalence ratios for factors associated with abnormal anal cytology [ ‡ atypical squamous cells of undetermined significance, (ASC-US)]. Characteristics of the 863 participants included: median age 42 years, 57% non-white, 79% current CD4 + T-cell count > 350 cells/mm 3 , 53% HIV-1 viral load < 50 copies/mL, median ART duration 5.8 years. Fifty-one percent of anal specimens contained ‡ 1 HR-HPV genotype; 31% had abnormal anal cytology [14% ASC-US, 11% low-grade squamous intra-epithelial lesion, (LSIL); 2% atypical squamous cells-cannot exclude high-grade SIL (ASC-H); 4% high-grade SIL/cancer (HSIL + )]. In multivariate analysis, cervical LSIL + , nadir CD4 + T-cell count £ 50 cells/mm 3 , HIV-1 viral load ‡ 50 copies/mL, and anal HPV 6,11,16,18,33, 45, 52, 56, and 58 were associated with ‡ anal ASC-US ( p < 0.05). Abnormal anal cytology and HR-HPV prevalences were high. HIVinfected women with cervical LSIL + , low nadir CD4 + counts, or detectable HIV-1 viral loads should be a particular focus for enhanced anal SCC screening efforts.