One hundred one squamous cell carcinomas (SCC) (study group) and 116 tissues without SCC or papilloma from matched anatomic sites (control group) were evaluated for the presence of human papillomavirus (HPV) DNA. Squamous cell carcinomas of the tongue (18%), tonsil (29%), and pharynx (13%) specifically harbored HPV-16-related sequences. In contrast, the nose, mouth, and esophagus proved completely negative. In the larynx, a low prevalence of HPV-11/16-related DNA was found in both cancers (5%) and control tissues (4%), suggesting that the associations lacked specificity. Our results indicate that anatomic site plays a role in determining the susceptibility to infection, and that the clinical entities with which HPV infections are associated include both subclinical infection with no history of papilloma, and malignant disease.