Lichen sclerosus (LS) is a skin disease that may affect both sexes at all ages and at any site. Its etiology remains unknown. The observation of focal koilocytotic-like changes in the stratum malpighii in prepuce samples of LS in children prompted us to investigate the presence of HPV-DNA. Twenty-three paraffin-embedded samples of LS lesions from children aged 4 to 14 years were studied using nested-PCR and in situ hybridization (ISH). Twelve out of 23 cases amplified HPV-DNA (8 cases corresponded to HPV-DNA type 6; 2 cases each to HPV-DNA types 16 and 18). ISH detected HPV sequences in the nuclei of koilocytotic and some parakeratotic cells in 13 cases (9/13 also HPV-DNA positive by PCR). Our results demonstrated the presence of HPV-DNA in roughly 70% of cases of LS of the prepuce in children. We highlight the observation of koilocytotic-like changes in the prepuce and its association with HPV. The possible pathogenetic significance between the virus and the lesion is not settled.