The mortality of squamous cell carcinoma of the tongue has not significantly improved in decades. Much of the information that has been gathered to date has been based on retrospective analyses. There is little consensus on treatment of the disease. In an attempt to define an objective prognostic indicator of aggressiveness of these tumors, a retrospective analysis of 15 paraffin-embedded specimens using flow cytometry was performed. Ten patients (67 percent) had aneuploid tumors and had a 5 year disease-free survival rate of 33 percent, whereas patients with diploid tumors (33 percent) had a 5 year disease-free survival rate of 80 percent. Although the number of patients was small, it appears that flow cytometry may be an objective prognostic indicator in patients with squamous cell carcinoma of the tongue. Larger series of archival paraffin-embedded flow cytometry analyses are recommended, as well as examination of variables other than the disease-free survival rate.