The ATP6V1C1 gene encodes the C1 subunit of the vacuolar-ATPase (V-ATPase) proton pump. This gene is over-expressed in oral squamous cell carcinoma (OSCC) as determined by real-time quantitative polymerase chain reaction. The aim of our study was to perform an immunohistochemical study of the distribution of the C1 subunit in normal epithelium of the oral cavity and in OSCC. We analyzed the expression of the C1 subunit in eight OSCC samples and two normal oral mucosa samples using polyclonal V-ATPase C1 antibody (clone H-300). In the normal oral mucosa samples, C1 subunit staining was observed in the basal and intermediate layers of the epithelium. No staining was visible in the keratinized superficial layers. More intense staining was observed in the OSCC samples, with the predominant expression at the periphery of tumor nests and absence of expression in dyskeratotic areas. C1 subunit expression in tumor cells was predominantly cytoplasmic, although there was perinuclear and nuclear expression in some samples. These findings demonstrate that V-ATPase is necessary for proper epithelial functioning and show its importance in the development of OSCC as evidenced by the over-expression of ATP6V1C1 in OSCC.