Liver transplantation is an effective treatment for patients with end-stage autoimmune liver diseases such as primary biliary cirrhosis, primary sclerosing cholangitis and autoimmune hepatitis. Clinical presentation of autoimmune liver diseases varies from acute liver failure to progressive development of end-stage liver disease and its complications. Indications for liver transplantation in autoimmune liver disease do not differ substantially from those used for other acute or chronic liver diseases. Despite the good reported outcomes, the recurrence of autoimmune liver disease is relatively common after liver transplantation, with incidence reaching up to 40%. The combination of clinical, laboratory and morphological tests are required, to establish the diagnosis of recurrent autoimmune diseases, however it may represent a challenge due to specific entities in transplant population such as acute graft rejection, viral hepatitis and even de novo autoimmune hepatitis. An awareness of the existence of recurrent autoimmune liver diseases in the allograft has important clinical implications on both immunosuppressive or non-immunosppressive treatment approaches, preventing or decelerating disease progression and reducing potential complications. The aim of this paper is to review the present knowledge of autoimmune liver diseases within the context of the transplantation, overviewing the incidence, risk factors, diagnostic criteria and treatement options, as well as outcomes for patients after transplantation.