Oral submucous fibrosis (OSF) is a high-risk precancerous condition of the oral cavity. Areca nut chewing is its key etiologic factor, but the full pathogenesis is still obscure. In this study, microarray analysis was used to characterize the mRNA changes of 14,500 genes in four OSF and four normal buccal mucosa samples to identify novel biomarkers of OSF. Five candidate genes with the most differential changes were chosen for validation. The correlation between clinicopathologic variables of 66 OSF patients and the expression of each gene was assessed by immunohistochemistry. The microarray analysis showed that 661 genes were up-regulated (fold value >2) and 129 genes were down-regulated (fold value <0.5) in OSF (q < 0.01). The top three up-regulated genes [Loricrin, Cartilage oligomeric matrix protein (COMP), Cys-X-Cys ligand 9 (CXCL9)] with the largest fold changes and the top two down-regulated genes [keratin 19 (KRT19), cytochrome P450 3A5 (CYP 3A5)] with the most significantly differential changes in OSF were chosen as candidate biomarkers. In immunohistochemical results, the expression of Loricrin and COMP showed statistically significant association with histologic grade of OSF (P = 0.03 and 0.006, respectively). COMP was found to be overexpressed frequently in patients with the habit of areca nut chewing for more than 4 years (P = 0.002). CYP 3A5 was revealed an inverse correlation with histologic grade (P = 0.04). This pilot study showed that five novel genes might play important roles in the pathogenesis of OSF and may be clinically useful for early detection of OSF.