The multidrug resistance-associated protein 3 (MRP3) is a multi-specific anion transporter that is capable of transporting a number of conjugated and unconjugated bile acids. Expression of the MRP3 gene is increased during pathological states associated with elevated bile acid concentrations indicating a role for this transporter in adaptive and homeostatic bile acid metabolism. Analysis of MRP3 mRNA levels in various mouse tissues with known relevance and/or exposure to bile acids revealed the highest levels of basal expression in the colon followed in order by the liver, duodenum, jejunum, ileum and kidney. Functional analysis of a murine MRP3 promoter reporter construct revealed vitamin D receptor (VDR)-dependent activation by 1,25-dihydroxyvitamin D3 (VD3), 9-cis retinoic acid (RA) and the cholestatic secondary bile acid, lithocholic acid (LCA). Using a series of deletion constructs combined with sequence analysis, a candidate VDR response element (VDRE) was identified between –1028 and –1014 bp of the MRP3 promoter. Activation of the MRP3 promoter in response to VD3, RA or LCA, as well as binding of VDR/RXR heterodimers, was attenuated substantially by mutation of this VDRE. Treatment of mice with VD3 or LCA demonstrated in vivo modulation of the MRP3 gene in colon but not in the liver. Reduction of endogenous VDR expression in colon adenocarcinoma MCA-38 cells by siRNA transfection was associated with reduced constitutive and inducible expression of the MRP3 gene. These data support a regulatory role for the VDR in the protection of colon cells from bile acid toxicity through regulation of the MRP3 expression.