BACKGROUND The cytokeratin (CK) pattern is accepted to be characteristic of a given epithelial cell or tissue. Specific changes in the CK pattern or in the expression of individual CKs may be characteristic in the early development of particular epithelial pathologies. Up to now no systematic hybridohistochemical study on the expression of CKs in normal human esophageal epithelium has been performed. Nevertheless, this knowledge may be of great importance for further research concerning the understanding of the structure and differentiation of normal esophageal epithelium and of the development of non-neoplastic and neoplastic esophageal malignancies. Therefore, we investigated the expression and distribution of nine different CK mRNAs throughout the normal human esophageal mucosa. METHODS A non-radioactive in situ hydridization protocol was used to study the expression of CK mRNAs in fixed and paraffin-embedded human esophageal mucosa. Digoxigenin-labelled cRNA probes were produced by in vitro transcription of cDNA clones, coding for human CKs. RESULTS In situ hybridization and immunodetection of the hybrids revealed a distinct but different distribution pattern for each specific CK mRNA. The described signal pattern was consistently found at all levels of the esophagus. We observed differences in the expression of some CK mRNAs between the interpapillar and papillar compartment of the esophageal epithelium. Mainly in the papillar regions some mRNAs are already expressed in more basally located cells in comparison with the interpapillar regions. Our results substantiate the hypothesis concerning the formation of papillae in the esophageal mucosa. We have also described some observations on the expression of CK mRNAs in fortuitous sections through excretory ducts of esophageal submucosal glands. CONCLUSIONS The distinct, characteristic, and reproducible distribution pattern observed for each specific CK mRNA indicates that the expression of the genes encoding CKs in the esophageal epithelium as well depends on the cell proliferation, on vertical cell migration and differentiation, and on detachment from the basal lamina. The results presented should be considered as complementary to the already existing immunohistochemical results concerning the distribution of esophageal CK proteins.