The level of expression of genes encoding for nine major xenobiotic metabolising Cytochrome P450s (CYPs) and the P-glycoprotein (Pgp) was determined in three different regions of the small intestine of male and female Sprague Dawley rats and the expression was compared with that in the liver. A semi-quantitative RT-PCR method, using the total RNA from the tissues, was established for the determination of the level of gene expression. Four of the CYP genes: the CYP2B1, CYP2C6, CYP2C11 and CYP2D1 and the Pgp were expressed at as high levels in the small intestine as in the liver. The expression of the other CYP genes was remarkably different in the two organs. The CYP1A2, CYP2A3, CYP2E1 and CYP3A1 showed a strong expression in the liver but only a comparatively weak or no expression in the small intestine. The CYP1A1 on the other hand exhibited a stronger expression in the small intestine than in the liver. With the exception of the CYP2A3, none of the genes showed a clear regional distribution in their small intestinal expression. Furthermore, no obvious sex difference in the expression of the CYP and Pgp genes could be observed. Our results indicate that several of the enzymes, central for drug metabolism are differently expressed in the liver and in the small intestine of the rat which should be taken into account when using rat as a model for the bioavailability and organ specific toxicity studies of orally administered xenobiotics. The apparently strong small intestinal expression of the CYP2C genes suggests that these enzymes could play a key role in the intestinal drug metabolism in rats and therefore affect the bioavailability of those orally used drugs which are substrates of the CYP2Cs. This possibility should be investigated in more detail both in rats and humans.