Papanicolaou (Pap)-stained cervical specimens from 160 squamous lesions were processed for the detection of human papillomavirus (HPV) DNA by an in situ hybridization (ISH) assay. Three biotinylated HPV DNA probes were employed, each containing HPV genotypes 6/11, HPV genotypes 16/18, or HPV genotypes 31/35/51. The HPV etiology of 86 lesions was ascertained (53.8%). In 74 out of 135 (58.8%) HPV-typed low-grade squamous intraepithelial lesions (SILs), HPV 6/11 was found in nine (6.6%), HPV 16/18 in 46 (34.2%), and HPV 31/35/51 in 19 lesions (14.1%); in 11 out of 18 HPV-typed high-grade SILs (61.1%), seven lesions (38.9%) were typed for HPV 16/18 and four (22.2%) for HPV 31/35/51. Of seven invasive carcinomas, only one (14.3%) reacted with the HPV 16/18 DNA probe. A cohort of 124 low-grade SILs were followed cytologically for a year. The results of this study are discussed in light of HPV type association and therapy.