Developmental studies have shown that morphological and functional regionalization occurring along the mammalian intestine is defined at early fetal stages and that some aspects of this patterning are dependent on epithelial-mesenchymal cell interactions. The molecular basis of these processes are largely unknown. In this study, a differential display approach was used to identify genes differentially expressed along the longitudinal axis in the intestinal endoderm and mesenchyme moieties of 14-day-old rat fetuses at a stage prior to morpho-functional differentiation of the gut. Fifty-eight genes were identified, 36 being identical or similar to known genes and 13 corresponding to ESTs or genome sequences with unknown function. Nine cDNAs could not be assigned to any previously described nucleotide sequence. The selected genes are involved in several aspects of cell physiology, including metabolic pathways, cytoskeleton organization, signal transduction, protein biosynthesis, and regulation of gene transcription.