Background. Approximately 90% of all anal cancers are associated with human papillomavirus (HPV), especially high-risk genotypes such as HPVs 16 and 18. Objective. To investigate the clinical and prognostic aspects of anal cancers associated with the presence, as well as the genotypic distribution of human papillomavirus (HPV). Methods. A retrospective study carried out over a 10-year period, using clinical and molecular data, with PCR analysis and reverse hybridization (INNO-LIPA kit), in anal cancers. The data analysis was done using descriptive univariate statistics, and the survival curves were made using the Kaplan–Meier and log-rank methods. Results. Of the 81 formalin-fixed and paraffin-embedded specimens, HPV prevalence was 69% and was significantly higher in squamous cell carcinomas (SCC) than in other anal tumors (p=0.0001). Female patients had a higher prevalence of HPV (p=0.01). Multiple infections were detected in 14.3% of cases. The most prevalent genotypes were HPVs 16, 33, and 18. The overall survival at 60 months was 44.3%, and the prognostic factors included gender (p=0.008) with greater survival for men (52.9%) in comparison to women (29.6%), histological type (p=0.01), SCC (54.4%), adenocarcinomas (37.5%), other carcinomas (14.2%), and the presence of distant metastasis (p=0.01). Survival was not influenced by the presence of HPV (p=0.54). Conclusions. The association of HPV to anal cancer was found in this study, especially in SCC. However, the presence of HPV did not influence the prognosis of patients with anal cancer.