Human autoimmune cholangiopathy comprises several intractable liver diseases that ultimately lead to hepatic failure. Primary biliary cirrhosis (PBC), allograft rejection, graft versus host diseases, and, possibly, primary sclerosing cholangitis are representative of immune-mediated cholangiopathies. Among them, PBC is the best-investigated human autoimmune cholangiopathy. The immunological approach to PBC has provided much critical information regarding its pathogenesis. The breakdown of self-tolerance in both B cells and T cells toward E2 components of the pyruvate dehydrogenase complex is evident. However, a number of questions regarding its etiology are unclear, in particular, the mechanisms involved in the selectivity of cholangiocyte destruction. In this brief review, we discuss what we know and we do not know regarding the pathogenesis of PBC.