Hepatocyte nuclear factor 6 (HNF-6) is a member of the one cut family of transcription factors and potentially regulates expression of numerous target genes important for hepatocyte function. In the liver, HNF-6 is expressed not only in hepatocytes, but also in biliary epithelial cells (BEC). To evaluate the in vivo function of HNF-6, we examined the hepatic expression pattern of HNF-6 messenger RNA (mRNA) and protein after bile duct ligation (BDL)-mediated liver injury. We found that HNF-6 protein levels in BEC and hepatocytes were diminished within 15 hours of BDL injury and remained suppressed through the fifth day of injury. The onset of BEC proliferation in response to bile duct obstruction was associated with diminished HNF-6 protein levels. To maintain hepatic HNF-6 protein levels during BDL liver injury, we used mouse tail vein injections with recombinant adenovirus expressing HNF-6 complementary DNA (cDNA) (AdH6). We found that maintaining hepatic HNF-6 levels with AdH6 infection resulted in significant decreases in BEC proliferation at 15 and 24 hours after biliary obstruction compared with adenovirus control. Our results showed that HNF-6 expression is diminished in BEC and hepatocytes and that maintaining hepatic HNF-6 expression hinders the normal biliary proliferative response to bile duct injury. This suggests that diminished hepatic HNF-6 levels are required for repair in response to biliary injury and that it regulates expression of genes that possess differentiation-specific function that are inhibitory to proliferation. In conclusion, we propose a biologic role for diminished HNF-6 protein levels in bile duct disease.