The prevalence of human papillomavirus (HPV) types 16 and 18 in clinical samples of squamous cell carcinomas from respiratory and upper digestive tracts was studied. HPV DNA of types 16 and/or 18 was detected using the polymerase chain reaction (PCR) method in 16 out of 121 cases (13.2%). By Southern blot hybridization, however, only the DNA from a laryngeal and a tonsillar carcinoma was found to hybridize with the whole HPV 16 DNA probe (two out of 16 HPV DNA-positive cases by PCR, 12.5%). None of the DNAs hybridized with the whole HPV 18 DNA probe. The discrepancy in the results of PCR and Southern blot hybridization methods seemed to reflect their sensitivity. The possible relation between prevalence of HPV DNA and carcinogenesis in respiratory and upper digestive tract is discussed.