The association of Human Papillomaviruses (HPV) DNA with female genital lesions has been widely documented whereas little has been reported about male genital pathologies. The aim of this work was to investigate the presence of HPV DNA and the genotype involved in male dysplastic genital lesions. All samples were analysed by polymerase chain reaction (PCR) to amplify HPV E1 and L1 genes. The PCR products were subjected to restriction fragment length polymorphism (RFLP) to determine the HPV genotype. We analysed 209 male genital biopsies from different lesions: mostly from acuminate condylomata and from Buschke-Lowenstein tumours, Bowen papulosis, leukoplakia of the glans, scrotal lymphangioma, penile horn and penile/perianal verrucous carcinoma. Our results revealed the constant presence of viral DNA in genital condylomata, mainly associated with low risk HPV; the presence of the same genotypes was also detected in some of the examined rare pathologies.