Tissues from 32 women with multicentric squamous cell neoplasia of the anogenital region (72 anatomically distinct lesions at the cervix, vagina, vulva, perineum, or anus) were tested for the presence of human papillomavirus with the polymerase chain reaction or in situ hybridization. All the women had invasive carcinomas or grade 3 intraepithelial neoplasia lesions at a minimum of one site and one or two squamous cell lesions at another site(s). Human papillomavirus was detected in all of the multicentric lesions in 87.5% (28/32) of the women and in at least one lesion in 12.5% (4/32). In the 28 women with detectable human papillomavirus at all sites, 61% (17/28) had the same virus type(s) at all sites (types 6, 16, 6 and 16, 33) and 25% (7/28) had 6 or 16 at one site and both viruses at the other site(s). Four women (15%) had different virus patterns in the separate lesions.