In cases with severe middle ear disease, transplantation of cultured mucosal epithelium is a useful as a way to promote regeneration of the mucous membrane on the bone surface exposed in middle ear surgery. In clinical practice, the middle ear mucosal membrane can be transplanted with the mucosal epithelium obtained from the nasal or oral mucosa as sampling areas for the epithelial cells. However, whether the transplanted epithelial cells derived from a surrogate tissue will perform as epithelial cells of the middle ear mucous membrane still remains unknown. In the present study, based on the epithelial-mesenchymal interaction, we hypothesized that the phenotype of the nasal and oral mucosal epithelial cells is converted to the phenotype of the middle ear mucosal epithelial cells by the microenvironment produced by the fibroblasts in the middle ear mucous membrane. In this study, we co-cultured epithelial cells and fibroblasts in vitro and performed a gene expression analysis using oligo DNA microarrays and quantitative real-time PCR. The results revealed that each of the epithelial cells has a different phenotype and that this phenotypes approximates to the epithelial cell phenotype of the middle ear mucous membrane upon co-culture with middle ear fibroblasts. In conclusion, it is suggested that the transplanted epithelial cells phenotype might be induced to change to the specific phenotype of the middle ear mucous membrane by the micro-environment.