To assess the prevalence of HPV infection in the genital tracts of women with normal PAP smears, a random series of 109 women was reexamined using colposcopy, a further PAP smear, and punch biopsies taken from the cervix (in 33 cases), vagina (212 cases), and anus (20 cases). The biopsy material was examined using routine histological investigations, in situ hybridization (ISH) with a 35S-labelled DNA probe cocktail (HPV 6, 11, 16, 18), and the polymerase chain reaction (PCR) to detect HPV DNA. Changes consistent with HPV infection were seen in 6.9% (18/262) of the biopsy specimens. Seven biopsy specimens (2.7%) from seven different women were found to contain HPV DNA using ISH. All of these ISH-positive lesions were diagnosed as morphologically characteristic HPV lesions: six flat condylomas and one papillary condyloma. Using PCR, the HPV DNA detection rate was highest in the cervical biopsy specimens (50%) and lowest (28.6%) in the anal biopsy specimens. A total of 35.5% of the 93 biopsy specimens studied using PCR contained HPV DNA. The commonest type was HPV 11 (54.5%), followed by HPV 18 (33.3%). Four of the nine biopsy specimens (44.4%) from colposcopically normal areas proved HPV DNA-positive using PCR. Of 17 biopsy specimens in which the histology was normal, seven were examined using PCR and three were DNA-positive. The discovery of HPV DNA using PCR in 32/92 of the biopsy specimens (34.8%) which had been found to be HPV DNA-negative when routine ISH was used is noteworthy. The results suggest that the light microscopy criteria currently used in diagnosing HPV infections are of no value in predicting latent HPV infections and that acetowhite staining is unable to distinguish between subclinical and latent infections on the one hand and changes unrelated to HPV on the other.