HIV and human papillomavirus (HPV) coinfection is increasing, especially in the anal canal (AC) and cervico-vaginal regions. We identified anal epithelium abnormalities related to high-risk HPV (HR-HPV) lesions in the lower genital tracts (LGTs) of HIV-positive women, described the HPV genotypes identified, and assessed the expression of E6/E7 oncogenes in coinfected patients. Ninety-eight women were enrolled in groups combining HIV status and presence or absence of HPV in the LGT. Anal and cervical smears were collected for cytology and HR-HPV assays using Cobas(®) and/or PapilloCheck(®). Samples with highly oncogenic HPV genotypes were confirmed by NucliSENS EasyQ(®). Forty-two HIV-positive (25-52; mean age 39.5) and 56 HIV-negative (18-58; mean age 35.7) patients were included. E2 and C1 groups presented AC alterations (P = 0.002); altered images for high-resolution anoscopy were higher in E1 and C2 (P < 0.001). Of the 29 women with alterations, 41.38% were HIV-negative and 58.62% were HIV-positive (P < 0.001). HIV-positive patients accounted for 29% of the anal high-grade squamous intraepithelial lesions (P = 0.015). The Cobas(®) positive result frequency was higher in three AC groups than in the other groups. There was variation in the number of HPV types in the cervico-vaginal samples among the study groups (P < 0.001). Anal cytology and anoscopy showed more altered findings in HIV-positive patients with HPV in the LGT. HR-HPV anal infections by various genotypes are common and are associated with cervical infections in HIV-positive patients. E6/E7 expression is apparently more common in the AC of HIV-positive women.