Invasive-squamous-cell-cancer (ISCC) of the anal canal is an uncommon disease. Human papillomavirus (HPV) is the etiological agent of most of types of ISCC. The incidence of ISCC has been increasing in HIV-infected individuals, even after the introduction of highly active antiretroviral therapy. The aim of this study was to analyze biopsy specimens from patients diagnosed with ISCC at a tertiary hospital from 1983 to 2012 in order to detect HPV-DNA. Methods: Formaldehydefixed, paraffin-embedded specimens from patients with ISCC underwent HPV-DNA genotyping using multiplex PCR assay. Results: A total of 31 cases were collected; 10 were HIV-infected (9 men, 1 woman) and 21 non-HIV-infected (11 men, 10 women). HPV infection was detected in 87.5% (7/8) of the HIV-infected patients (DNA from 2 biopsies was degraded) and 76.2% (16/21) of non-HIVinfected individuals. Multiple-type infections were only found in 28.6% (2/7) of the HIV-infected * Corresponding author. L. Darwich et al. 1156 patients (no multiple-type infections in non-HIV-infected individuals). The most prevalent type was HPV-16: 50% (4/8) in the HIV-infected group (57% [4/7] of the HPV-positive samples) and 66.7% (14/21) in the non-HIV-infected group (87.5% (14/16) of the HPV-positive samples). Remarkably, 37.5% (3/8) of the HIV-infected group had high-risk HPV types not included in the vaccines (HPV-33, 51, 52, and 66) compared with 4.8% in the non-HIV-infected group (1/21, HPV-52). All cases of anal ISCC in HIV-infected patients were recorded in the highly active antiretroviral therapy era. Conclusion: HIV-infected patients presented anal ISCC with a higher proportion of high-risk HPV types not covered by the conventional vaccines than non-HIV-infected individuals.