Investigating the prevalence of high-risk human papilloma virus (HPV) genotypes in human immunodeficiency virus (HIV)-infected women is vital to generate data for formulating guidelines for prevention/screening of cervical cancer in this vulnerable group. The study was aimed to analyze the HPV genotypes in HIV-infected women. It was a prospective, hospital-based, and cross-sectional study. HIV-infected women were enrolled from the antiretroviral clinic and controls from the gynecology outpatient. The HPV genotyping array kit was used for identifying 21 HPV genotypes. Detection of HPV was confirmed by performing an HPV type-specific polymerase chain reaction. A Pap smear was collected in all women. One hundred thirty HIV-infected women and 64 controls were enrolled. All women with low CD4 counts (n=97) were receiving antiretroviral therapy. Twenty-six (20%) HIV-infected women and 12 (18.7%) women in the control group tested positive for high-risk HPV (P=1.0). HPV 16 was the most common type, detected in 42% of HPV-positive women in the HIV-infected cohort, followed by HPV 45 (15%), HPV 18/52/31/58 (11.5% each), and HPV 33 (7.6%). The corresponding figures in the control group were as follows: HPV 16 (66.6%), HPV 45/18/31 (16.6% each), and HPV 33/58/68 (8.3% each). Cervical intraepithelial neoplasia was detected in 2.3% of HIV-infected women. The prevalence of high-risk HPV in HIV-infected women (20%) was similar to the prevalence in controls (18.7%). This and the incidence of cervical intraepithelial neoplasia are lower than those in previous reports. It is plausible that administration of antiretroviral therapy contributed to the reduced prevalence. The currently available vaccine would likely be beneficial to the local HIV-infected population, as nearly half the HPV-infected women harbored genotypes 16 or 18.