Although oral submucous fibrosis (OSF) is the most common precancerous lesion of the oral cavity in Southeast Asia where the habit of betel quid (BQ) chewing is popular, its molecular biological properties are largely unknown. The aim of this study was to identify the genes responsible for its pathogenesis and malignant transformation using oligonucleotide microarray. The expression profiles of 14,500 genes in human oral submucous fibrosis and normal control were analyzed using Affymetrix U133A 2.0 GeneChip arrays. The results revealed that 716 genes were upregulated and 149 genes were downregulated in OSF. Hierarchical clustering revealed that the gene expression profiles of normal and OSF were clearly distinct by these different expression genes. Gene Ontology (GO) and relevant bioinformatics tools identified a list of significant differentially expressed genes involved in immune response, inflammatory response and epithelial-mesenchymal transition (EMT) induced by TGF-beta signaling pathway. Five EMT-related genes including SFRP4, THBS1, MMP2, ZO-1, and CK18 were validated with RT-PCR. Our data suggested that gene abnormalities in immune response, inflammatory response and EMT induced by TGF-beta might play an important role in the pathogenesis and malignant transformation of OSF.