Primary biliary cirrhosis (PBC) and primary sclerosing cholangitis (PSC) belong to the group of liver diseases which are believed to be caused by autoimmune reactions. The primary causes of these diseases remain unknown. However, thanks to the recent studies in immunogenetics, progress has been made in understanding the mechanisms underlying these pathologies. Moreover, studies are being held on identification of specific autoantigens in these diseases. The results of these studies are criteria of diagnosis and treatment of those diseases. As there is still no specific treatment of PBC and PSC, in many cases best results are achieved with allogenic orthotropic liver transplantation.