In most studies concerning chromosomal changes or protein expression in head and neck squamous cell carcinomas (HNSCC) no distinction is made between the sites within this area. The behaviour of tumors arising in one site or the other, however, differs significantly, suggesting different intrinsic tumor properties. In this study we compared the expression of several proteins (p53, Rb, cyclin D1 myc, bcl-2, EGFR, neu, E-Cadherin, Ep-CAM, Desmoplakin1 and nm23) in the three major sites of HNSCC (larynx, pharynx, and oral cavity). Expression of the proteins was studied by immunohistochemistry in 33 laryngeal, 31 pharyngeal and 36 oral carcinomas. Cyclin D1 had a very high level of expression in the pharynx (p = 0.0004) and EGFR very low in the larynx (p < 0.0001) compared to the other sites. To a lesser degree p53 (p = 0.05), Desmoplakin1 (p = 0.04) and Ep-CAM (p = 0.02) showed statistically nearly significant differences. For the other proteins no statistically significant difference in expression was found. These results show that the expression of a number of proteins is not identical in the three major localizations of HNSCC and indicate the different tumor biology of cancers originating from different sites in the Head and Neck. It is therefore not justified to consider the different localizations as one entity. Moreover, these differences may have clinical and prognostic relevance.