Human papillomavirus (HPV) DNA has been detected in approximately 15% of squamous cell carcinomas (SCCs) of the head and neck. Recent studies have shown a predilection of HPV for certain anatomical sites, especially the tonsillar region, with viral DNA identified in approximately 60% of SCCs of the Waldeyer's tonsillar ring. This study was undertaken to determine whether there are differences in morphology or in oncogene expression in SCC of the tonsil with and without detectable HPV DNA. Twenty-two SCCs of the tonsil were analyzed for the presence of HPV DNA by polymerase chain reaction (PCR) using both a consensus primer set (My09/My11) and type-specific primers. Viral transcription was established in both primary and metastatic tumors by RNA in situ hybridization. The morphology of invasive SCC was classified into three subtypes: well keratinized (K-SCC), intermediate keratinized (I-SCC), and poorly keratinized (P-SCC). Expression of p53, pRB, and cyclin D1 (bcl-1) were studied by immunohistochemistry. In these cases (6 K-SCCs, 2 I-SCCs, and 14 P-SCCs), HPV DNA was detected in 14 (64%), with 11 containing HPV-16 (10 P-SCCs, 1 I-SCCs, and 0 K-SCCs) and 1 each containing HPV-33, HPV-59, and an unclassified HPV type (all P-SCCs). Viral oncoprotein E6/E7 transcription was demonstrated in 7 of 7 HPV-16-positive tumors. Cyclin D1 protein overexpression was detected in the majority of HPV-negative tumors (7 of 8 cases), whereas it was minimal or absent in 13 HPV-positive tumors. Overexpression of p53 protein was detected in 3 HPV-negative K-SCCs. In the HPV-positive tumors, fewer malignant cells expressed pRB and the staining was less intense than in the HPV-negative cancers. HPV DNA and E6/E7 expression, especially HPV-16, is detected in the majority of tonsillar SCCs and is almost exclusively associated with a poorly keratinized tumor histology. Decreased expression of cyclin D1, pRB, and p53 in tumors with HPV DNA is consistent with the known effects of the viral oncoproteins on the cellular protein. The morphology of the HPV-positive tumors suggests that HPV may have a predilection for a population of nonkeratinizing squamous cells or that the virally transformed cells inhibit keratinization of the tumor cells. Well keratinized tonsillar SCCs lack HPV DNA and are associated with overexpression of cyclin D1 protein and/or p53, suggesting that mechanisms that alter the cell cycle regulatory proteins, either by interaction with viral oncoproteins or by changes in the cellular proteins themselves, is critical for tumorigenesis of tonsillar SCC.