We previously established an in vitro cellular carcinogenesis model of oral squamous cell carcinoma (OSCC) with a line of human immortalized oral epithelia cells (HIOECs), a line of cancerous HB96 cells, and other cells (HB56 cells) at the early stage of carcinogenesis. In this study, comparative proteomic analysis identified a panel of differentially expressed proteins among these cells, and S100A6 was shown as one of the significantly down-regulated proteins accompanying cellular transformation. S100A6 was further validated for its expression in the three cell lines and in the clinical samples of cancerous and paracancerous tissues from 30 primary OSCC patients. Western blot analysis and real-time PCR revealed the decreased S100A6 protein and mRNA levels in the cancerous HB56 and HB96 cells over HIOECs. Immunohistochemistry and real-time PCR also showed decreased S100A6 protein and mRNA levels in the cancerous tissues compared to the paracancerous tissues from OSCC patients. The results presented here suggest that the expression of S100A6 decreases along with the cancerization in OSCC both in vitro and in vivo.