The site-specific function of multidrug-resistance-associated proteins (MRPs), especially MRP2 and MRP3, was examined in rat intestine and human colon adenocarcinoma (Caco-2) cells. The MRP function was evaluated pharmacokinetically by measuring the efflux transport of 2,4-dinitrophenyl-S-glutathione (DNP-SG), an MRP substrate, after application of 1-chloro-2,4-dinitrobenzene (CDNB), a precursor of DNP-SG. The expression of rat and human MRP2 and MRP3 was analysed by Western blotting. The rat jejunum exhibited a higher apical MRP2 and a lower basolateral MRP3 expression than ileum. In accordance with the expression level, DNP-SG efflux to the mucosal surface was significantly greater in jejunum, while serosal efflux was greater in ileum. Site-specific bidirectional efflux of DNP-SG was also observed in in-vivo studies, in which portal and femoral plasma levels and biliary excretion rate of DNP-SG were significantly higher when CDNB was administered to ileum. Caco-2 cells also showed a bidirectional efflux of DNP-SG. Probenecid, an MRP inhibitor, significantly suppressed the mucosal efflux in jejunum and serosal efflux in ileum. In contrast, probenecid significantly suppressed both apical and basolateral efflux of DNP-SG in Caco2 cells, though the inhibition was of small magnitude. In conclusion, the efflux of DNP-SG from enterocytes mediated by MRPs exhibited a significant regional difference in rat intestine, indicating possible variability in intestinal bioavailabilities of MRP substrates, depending on their absorption sites along the intestine.