The expression of sucrase-isomaltase mRNA was investigated along the crypt-villus axis of rat small intestine using differentially isolated cells and in situ hybridization. A partial rat sucrase-isomaltase cDNA was cloned which coded for a protein that was predicted to be 88% homologous to those encoded by the rabbit and human cDNAs. Southern blot analysis of rat genomic DNA indicated that the cDNA hybridized to a single gene. Northern blots of RNA extracted from subpopulations of intestinal epithelial cells that were isolated from villus and crypt compartments showed that this cDNA hybridized to a 6.5 kb band predominantly in villus RNA. In situ hybridization using 35[S]-labeled RNA probes demonstrated that autoradiographic grains were detected over eptithelial cells located on villi with the greatest number of grains located at the crypt-villus junction and in the lower to mid-villus region; from mid-villus to the villus tip there was a decline in sucrase-isomaltase mRNA. We conclude that expression of sucrase-isomaltase as enterocytes emerge from intestinal crypts is regulated primarily at the level of mRNA accumulation which, most likely, is a result of activation of sucrase-isomaltase gene transcription.