Abstract Background The human papillomavirus (HPV) prevalence in males has been reported to be between 3.6% and 84%, depending specially on the socioeconomic status. HPV infection has been related as a risk factor for penile cancer. This is a rare tumor, and other risk factors include lack of personal hygiene and men who have not undergone circumcision. Penile cancer is less than 1% of cancers in men in the United States, however, is much more common in some parts of Asia, Africa, and South America, where it accounts for up to 10% of cancers in men. This study aimed to determine the prevalence of HPV-DNA in penile cancers in São Luís, Brazil and to correlate the virus presence to histopathological factors. Methods Tumor paraffin samples of 76 patients with penile carcinoma were tested in order to establish the prevalence and distribution of genotypic HPV using PCR/Nested and automated sequencing. To evaluate the association between HPV types and other clinical and morphological variables, a nonparametric ANOVA was performed using a Kruskal Wallis test, and statistical significance was determined to a value of p