Human papillomaviruses (HPV) have been detected in squamous cell carcinoma (SCC) of the aerodigestive tract with varying frequency of 10%-100% mainly due to detection methods and primer pairs used. Polymerase chain reaction (PCR) is the most sensitive and Southern blot hybridization (SBH) the most specific detection method of HPV DNA. Both methods achieve the most reliable results. 22 SCC DNA samples of the hypopharynx were analyzed by type specific and consensus primer PCR and Southern blot analysis. HPV was detected in 5/22 (22.6%) hypopharyngeal SCC specimens. HPV 18 and HPV 45 were identified in one case each. An HPV prevalence of 23% is a realistic approximation in hypopharyngeal SCC. The high rate of HPV positive only detected by non type specific detection methods indicates the presence of previously undescribed HPV types.