Human papilloma virus (HPV) can reach a child's anogenital area by vertical transmission or by close contact, which can be either sexual or nonsexual. Our objective was to compare HPV in prepubertal girls with and without lichen sclerosus (LS). We compared the frequencies and types of HPV in girls with LS with those in children with non-LS vulval disease (vulval swab and urine) and in children with no known vulval disease (urine only). HPV DNA was detected using a nested polymerase chain reaction (PCR) with general and consensus primers amplifying a region of the L1 gene, and PCR amplicons were typed using reverse hybridization with labeled HPV type-specific probes. Specimens untypeable by this method were typed by DNA sequencing. In the cohort of children with LS, we recorded the presence of maternal anogenital warts or a dysplastic cervical smear within 3 years of the affected child's birth. We found that HPV was present in the urine and vulval swabs of 8 of 32 children with LS and in 2 of 31 children with non-LS vulval disease, but also in the urine of 7 of 29 controls. In those with LS, the frequency was not increased significantly, but the types were predominantly those commonly associated with dysplasia of the cervix, penis, vulva, and anus, as opposed to the broader spectrum of types found in the control group, not all dysplasia associated. Two of the 32 mothers reported warts, and 15 of 32 (46.9%) had an abnormal smear. (The national average of abnormal cervical smears is less than 10%.) We concluded that HPV appears to be common in all prepubertal girls, but children with LS carried types associated with dysplasia and their mothers had had a high incidence of dyskaryotic smears.