To elucidate the mechanisms leading to the functional regionalization of the digestive epithelium, lactase expression was analyzed at the protein, mRNA and gene levels, along the intestinal tract at various stages of the rat postnatal development. In the colon of neonates, the transient expression of mRNA and enzyme correlated well with gene transcription. In contrast to the colon, complex patterns were observed in the small intestine. In suckling animals, the mRNA was present at a high level despite the progressive decline of enzyme activity. Crypts were devoid of mRNA and the transcript mainly accumulated in the lower half of the villi. From weaning onwards, a functional regionalization of the epithelium was defined, characterized by the modification of the longitudinal distribution of lactase mRNA. Indeed the transcript remained abundant in the distal duodenum, jejunum and proximal ileum, but decreased in the proximal duodenum and became virtually absent in the distal ileum. Concomitantly, the mRNA and enzyme distribution along the villi changed in the different segments of the small intestine. Patterns similar to those described in sucklings were retained in the adult jejunum. In contrast, mRNA and enzyme could no longer be detected in the distal ileum, while mosaicism appeared in the proximal duodenum. In vitro transcription assays carried out with isolated nuclei suggested that the decay of lactase mRNA in the proximal duodenum at weaning was associated with a decreasing rate of transcription of the gene. However active gene transcription was retained in the nuclei of the adult jejunum and ileum. The loss of mRNA in the adult distal ileum despite the maintenance of active transcription did not result from an intragenic block of pre-RNA elongation, as shown by transcription assays carried out at various positions of the lactase gene. In addition, we looked for the ontogenic decline of lactase protein despite the maintenance of a high amount of mRNA in the jejunum, and it became evident that the fraction of mRNA present in polysomes was constant with age. Taken together, these data indicate that lactase constitutes an unusual marker of development and of functional regionalization of the intestinal tract which exhibits a complex time- and space-specific pattern of gene, mRNA, and protein expression. The distinct patterns occurring in the duodenum, jejunum, ileum, and the colon of pre- and postweaned rats depend on a combination of transcriptional, posttranscriptional, and posttranslational levels of regulation. and are associated with a different mRNA distribution along villi in each intestinal segment.