It has been suggested that certain viruses such as human papillomaviruses (HPV) and Epstein-Barr virus (EBV) might have a role in oral squamous cell carcinoma (OSCC). However, results of the published studies are controversial and are dependent on the geographic distribution and methods of sampling and sample analysis. The aim of this study was to determine the prevalence of HPV 16 and EBV in OSCC patients. In 24 patients with OSCC (mean age 59.6 +/- 8.8) and 30 controls (mean age 49.1 +/- 8.3), 5 mL of blood was collected to determine the prevalence of EBV by serologic methods. In addition, swabs were obtained to analyze the presence of HPV 16 and EBV by use of polymerase chain reaction. Statistical analysis was performed by use of Mann-Whitney test, chi2-test and Spearman correlation test. The results of this study showed that there were no significant differences between OSCC patients and control subjects according to the presence of EBV or HPV 16. Therefore, it can be concluded that the role of the aforementioned viruses is less likely in our population of OSCC patients.