Bile ducts lined with biliary epithelial cells, or cholangiocytes, are the main components of the biliary system in liver. Cholangiocytes participate in the production and transport of bile substances, as well as participate in immune responses. Cholangiocytes protect against pathogens by expressing toll-like receptors and anti-microbial peptides; act as antigen-presenting cells by expressing human leukocyte antigen molecules and costimulatory molecules; recruit leukocytes to the target site by expressing adhesion molecules, cytokines, and chemokines; and induce apoptosis of leukocytes to limit the immune responses. Several cholangiopathies result from dysfunctions of the biliary system. They can broadly be divided into autoimmune, genetic, infectious, drug, and ischemic-injury-induced categories. The pathogenesis of many of these cholangiopathies is unclear and treatment is limited. Further understanding of the complexity of the biliary system is critical for medical advancements in this field.