To date, few studies have evaluated the diagnostic and prognostic potential of flow cytometry in oropharyngeal tumors. The purpose of this study was to evaluate the interrelationship of anatomic location with the cytogenetic and cytokinetic characteristics of squamous cell carcinomas of the posterior oropharynx. Forty-eight paraffin-embedded squamous cell carcinoma specimens from the posterior oropharynx in clinical stages I to IV were analyzed with an Epics-C flow cytometer (Coulter Diagnostics, Hialeah, FL). Histopathologic grading was performed by the same pathologist, based on tumor differentiation. Of the 38 specimens suitable for analysis, several correlations were noted. First, as the %S-phase increased, the clinical stage increased. Second, as the histologic grade increased, the aneuploid frequency increased. Finally, as the tumor size increased, the histologic grade increased. From the results of this study, it was concluded that %S-phase may be useful in assessing the prognosis of squamous cell carcinomas of the posterior oropharynx. DNA index or aneuploid frequency, also may have value as a prognostic indicator. Finally, the lack of correlation between TNM staging and histologic grading stems not from tumor size but from nodal and metastatic involvement. Further studies are warranted to better define the usefulness of flow cytometric analysis in squamous cell carcinomas of the oropharyngeal region.