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High-risk human papillomavirus (HPV) in a lesion is related to an increased chance of neoplasic transformation, especially when with immunosuppression, as in HIV infection. We investigated HPV frequency in cutaneous and mucosal lesions of HIV-seropositive male patients. The frequency of malignancy, its association with the HPV type detected and some clinical variables were also assessed. A total of 38 lesions from 27 patients were studied in a period of 18 months. The biopsied fragment was submitted to HPV detection and typification, through polymerase chain reaction with generic (MY09/11) and specific (types 6, 11, 16 and 18) primers. HPV frequency was 63.2%, with detection of HPV types 6, 11 or 16 in 18 lesions and with multi-infection in three. There was low detection of high-risk HPV (type 16, 18.4%) and no HPV type 18. Of the lesions, 36.8% were already premalignant or malignant, and the frequency of moderate or severe dysplasia was higher in the study patients than that described in the HIV-seronegative population. High-risk HPV (type 16) was detected in four benign lesions and low-risk HPV (type 6) in three premalignant genital lesions. There was no significant association between the clinical variables and an increase in the prevalence of premalignant or malignant lesions.