The Epithelial Cell Adhesion Molecule (EpCAM) is expressed virtually on normal epithelia in vertebrates. Among different species, the amino acid sequence of EpCAM is highly homologous, indicating that EpCAM is an evolutionary conserved protein. However, differences in the expression pattern of EpCAM homologues have been reported. We hypothesized that differences in expression pattern might be related to the promoter organization of the respective EpCAM homologues. Therefore, we here compared the promoter region of the mouse and human EpCAM homologues. In addition, we compared the expression pattern of the human and murine EpCAM homologues in the hEpCAM transgenic mouse. In silico analysis of EpCAM homologues revealed that the amino acid sequence as well as the domain structure is highly conserved throughout different vertebrates. In silico analysis of the promoter region identified that the human and mouse EpCAM promoters share a low homology. In agreement with this low homology, the murine and human EpCAM promoter contains only a few common transcription factor binding sites. Nevertheless, immunohistochemcial analysis of the expression of human and murine EpCAM in lung, colon, and kidney of the hEpCAM transgenic mouse identified that expression of both homologues is restricted to epithelial cells in these organs. Moreover, in lung and colon the human and murine homologues of EpCAM were co-expressed. In contrast, the EpCAM homologues were only sporadically co-expressed in renal epithelia, although they were distributed similarly along the nephronic segments. Together, these findings indicate an overall conserved regulatory mechanism that ensures epithelial expression of EpCAM homologues, despite the low promoter homology. Furthermore, the fact that murine epithelia express the human homologue of EpCAM indicates that the mouse has transcription factors required for human EpCAM expression.