To expand information regarding the epidemiology of genital human papillomavirus (HPV) infection in young girls, girls with external genital warts were examined for the prevalence of cervical-vaginal or intraanal HPV infection. Cervical-vaginal wash specimens and biopsies of external lesions were examined for HPV genotypes 1, 2, 4, 6, 11, and 16 using Southern transfer hybridization with restriction endonuclease fragment length analysis. Exfoliated cells from cervical-vaginal and intraanal canals were processed for cytologic study. Of 18 girls, 8 (44%) had cytologic or genomic evidence (or both) of cervical-vaginal or intraanal HPV infection. Five had cervical-vaginal wash specimens that were positive for HPV genome and showed mild dysplasia. As is true for adults, young girls with external anal-genital warts are also frequently infected with HPV at internal mucosal sites. Determining the immediate and long-term prognosis of infected children and those with intraepithelial neoplasia will require appropriate prospective studies.