P-glycoprotein is a multidrug transporter encoded by the mdr3 gene in the mouse intestinal epithelium. The aims of this study were to characterize the mdr3 gene expression in the cephalocaudal axis of the intestine in adult animals and during perinatal development, and to define the molecular mechanism responsible for the heterogeneous expression of the gene along the cephalocaudal axis. RNA extracted from stomach, duodenum, jejunum, ileum, cecum and colon was hybridized by slot blot and Northern blot using a mdr3 cDNA probe. The regulation of gene expression was investigated examining the rate of transcription by nuclear run-off analysis. Transport studies of rhodamine 123, a substrate of P-glycoprotein, were performed in everted jejunum and ileum. The level of mdr3 mRNA and P-glycoprotein found in ileum was 6-fold higher than the level found in duodenum. The regional pattern of mdr3 gene expression is established in the intestine of 10-day-old animals. Similar mdr3 hybridization signal in nuclear run-off assay was found in nuclei of enterocytes isolated from jejunum and ileum, suggesting that the heterogeneous expression of the mdr3 gene in the cephalocaudal axis of the small bowel may be predominantly regulated at the post-transcriptional level. Transport rate of rhodamine 123 from the serosal to mucosal side in everted ileum was higher than the rate of transport found in jejunum. These results indicate that enterocytes of the ileum may be more actively involved in the P-glycoprotein-mediated transport of xenobiotics into the intestinal lumen.