Cholangiocytes are epithelial cells that line the biliary tract and are also known as biliary epithelial cells (BECs). In vitro culture studies of BECs in correlation with tissue section examination may give us a comprehensive analysis of biliary tract diseases. Herein, we discuss genetic cholangiopathy of autosomal recessive polycystic kidney disease (ARPKD), mainly using a polycystic kidney (PCK) rat, an animal model of ARPKD. The hepatobiliary lesions in ARPKD patients (Caroli's disease and congenital hepatic fibrosis) and in PCK rats are speculated to be related to mutations to polycystic kidney and hepatic disease 1 (PKHD1) which have been recently demonstrated, though the exact causal relation between these mutations and hepatobiliary pathology remain to be clarified. Recently we clarified that BECs of PCK rat showed increased cell proliferation followed by irregular dilatation of intrahepatic bile ducts. We also identified the essential involvement of the MEK5-ERK5 pathway in the abnormal proliferation of BECs in the PCK rat. The degradation of laminin and type IV collagen (basal membrane components of bile ducts) was closely related to the biliary dysgenesis and cystogenesis in the PCK rats. BECs also showed mesenchymal phenotype followed by progressive portal tract fibrosis, indicating TGF-β1 may be involved in this acquisition of mesenchymal phenotype. Detailed tissue culture correlation studies of ARPKD and PCK rats are mandatory to evaluate the pathogenesis of this genetic cholangiopathy.