An innate immune response to bacterial and viral components is thought to be involved in the pathogenesis of cholangiopathies in case of primary biliary cirrhosis (PBC) and biliary atresia. Biliary epithelial cells possess the Toll-like receptor (TLR) family which recognizes pathogen-associated molecular patterns (PAMPs) and plays a pivotal role in the innate immune response. In PBC, disordered regulations of TLRs and a negative regulator of intracellular signaling, peroxisome proliferator-activated receptor-γ (PPARγ), with Th1-predominant cytokine milieu are involved in the pathogenesis of cholangitis such as chronic non-suppurative destructive cholangitis (CNSDC). Moreover, CD4-positive Th17 cells characterized by the secretion of IL-17, are implicated in the chronic inflammation of bile ducts in PBC and the induction of Th17 cells around bile ducts is causally associated with the biliary innate immune responses to PAMPs. In biliary atresia characterized by a progressive, inflammatory, and sclerosing cholangiopathy, dsRNA viruses could directly induce the expression of tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) and apoptosis in biliary epithelial cells as a result of the biliary innate immune response via dsRNA-recognizing receptors such as TLR3 and retinoic acid inducible gene I (RIG-I). Moreover, as a mechanism behind the sclerosing cholangiopathy in biliary atresia, epithelial-mesenchymal transition (EMT) has been proposed and the biliary innate immune response to dsRNA viruses is demonstrated to induce biliary epithelial cells to undergo EMT. Biliary innate immunity is associated with the pathogenesis of various cholangiopathies in biliary diseases as well as biliary defense systems.