DNA ploidy and cell-cycle distribution were determined by flow cytometry in fresh tumor tissue of 27 epithelial head and neck carcinomas. Epithelial cells were labeled with a fluorescein-isothiocyanate-conjugated cytokeratin antibody to study the possible influence of contaminating stromal and inflammatory cells on the results of cell-cycle analysis of tumor cells. The patient sample included 26 men and 1 women with a mean age of 60 years. Without cytokeratin gating, 11/27 tumors (40.74%) were aneuploid. After selecting the cytokeratin population, 10 more aneuploid tumors were found that had not been detected when considering the total population. Therefore, aneuploid tumors increased from 40.74% to 77.74%. The remaining 6/27 (22.26%) tumors were diploid. In the tumors that were either aneuploid without cytokeratin gating or diploid, the S-phase and G2M phase were significantly higher after cytokeratin staining, specially in diploid tumors (24.2% versus 10% and 6.8% versus 3.2%, respectively, p < 0.01). Therefore, in head and neck tumors cytokeratin staining optimizes both the determination of DNA ploidy and cell-cycle analysis, which is advantageous for tumor staging and prognosis assessment in these patients.