Oral squamous cell carcinoma (OSCC) is an aggressive malignancy. The five-year survival rate remains largely unchanged for the past 40 years. Early diagnosis has been shown to correlate with increased survival, based on cytologic changes. In order to improve our current treatment strategies for OSCC, it is necessary to understand the genetic and molecular networks underlying this disease. In this preliminary study, we illustrate the application of DNA microarrays to study OSCC. Using computational and statistical algorithms, we were able to differentiate (or classify) "cancer" and "normal" samples based on the behavior of the gene expression profiles. We found 651 genes to be associated with cancer. This article describes a preliminary study of current developments from the Human Genome Project (HGP) and its application to OSCC.