Endotoxin-mediated cholestasis stems from impaired hepatobiliary transport of bile acids and organic anions due to altered expression and activity of transporters, including Oatp, Mrp, Ntcp, and Bsep. However, the mechanisms by which the Oatp and Mrp genes are down-regulated are largely unknown. Using in vivo and in vitro murine models of inflammation, we examined the role of cytokines and bile acids in regulating Oatp and Mrp. Endotoxin (lipopolysaccharide, LPS), interleukin (IL)-6, IL-1beta, tumor necrosis factor (TNF)-alpha, cholic acid, taurocholate, or taurodeoxycholate was administered in vivo to mice or in vitro to Hepa 1-6 mouse hepatoma cells. Mrp, Oatp, and Bsep mRNA levels were measured by reverse transcription-polymerase chain reaction. Mrp efflux activity was measured using 5-carboxyfluorescein. In vivo, LPS treatment profoundly suppressed hepatic mRNA levels of Mrp2, Mrp3, Oatp1, Oatp2, and Bsep to 15, 60, 44, 30, and 32% of controls, respectively (p < 0.05), but did not significantly alter Mrp1 expression. IL-6 or IL-1beta administration suppressed Mrp2, Oatp1, Oatp2, and Bsep mRNA levels to 20 to 60% controls (p < 0.05). TNF-alpha administration affected mRNA levels of Mrp2, Mrp3, and Oatp2 but not Oatp1 or Bsep. Bile acid treatment increased the in vivo expression of Bsep but not Mrp or Oatp. Likewise, significantly lower mRNA levels of Mrp2 with a corresponding decrease in cellular efflux of 5-carboxyfluorescein was seen in vitro in IL-6- and IL-1beta-treated Hepa 1-6 cells, whereas bile acids did not have significant effects. In conclusion, cytokines are key mediators in regulating hepatic expression of anion transporters in inflammatory cholestasis, whereas bile acids likely play a minor role.