Oral squamous cell carcinomas represent more than 90% of all head and neck cancers, and comprise about 4% of all malignancies in western countries. Tumor cell mobility related to increasing intracellular pH results in impaired proliferation and metastasis, suggesting an important role of pH regulation in solid cancer tumorigenesis. The mechanism of physiological pH regulation has been shown to be activated in several solid tumors through constitutive activation of the ATPase complex. How cells regulate this mechanism has not been elucidated in human cancer in detail. The present study, using expression profiling by cDNA array analysis of oral squamous cell carcinoma cells, identified the V-ATPase system as a significant regulatory mechanism. ATP6V1C1 was the most strongly over-expressed gene in oral squamous cell carcinoma at the mRNA level compared to other genes of the V-ATPase complex. These findings provide evidence that intracellular pH regulation is mainly controlled by expression of a single gene, ATP6V1C1, notwithstanding the possible action of other secondary regulatory factors.