Human papillomaviruses (HPVs) have been etiologically linked to a subset of head and neck squamous cell carcinomas (HNSCCs), generally arising in young patients without a history of tobacco smoking or alcohol use. These tumors typically lack mutations in TP53 and may show enhanced sensitivity to chemoradiation therapy with a correspondingly better overall prognosis. The determination of the HPV status in HNSCC therefore has therapeutic implications. We compared the Ventana ISH iView Blue Plus Detection Kit in situ hybridization (ISH) system and the Roche Linear Array HPV Genotyping Test for the detection of HPV in 98 formalin-fixed, paraffin-embedded HNSCC samples. A moderate concordance rate (70.4%) was observed between ISH and the Linear Array assays. ISH detected HPV in 39.8% of cases, whereas Linear Array detected HPV in 57.1% of cases. Sensitivity and specificity of ISH for detecting HPV in HNSCC specimens were determined to be 58.9% and 85.7%, respectively, using the Linear Array as the method of comparison (McNemar test, P=0.003). ISH offers the advantage of visual cell-type localization of viral infection but overall it is less sensitive than the polymerase chain reaction-based detection of HPV in HNSCC. Copyright © 2011 by Lippincott Williams & Wilkins.