Autoimmune diseases of gastrointestinal organs require a timely diagnosis to facilitate appropriate treatment. It is an important challenge to differentiate autoimmune pancreatitis (AIP) from pancreatic carcinoma. This is hampered by the occurrence of focal changes in the pancreatic parenchyma in AIP. Additionally, lymphadenopathy and duct obstruction are present. Autoimmune hepatitis (AIH) results in liver cirrhosis and organ failure if not discovered in time. In 40 % of patients with AIH the initial diagnosis is not achieved at an early stage. Intestinal tuberculosis must be differentiated from Crohn's disease, especially if modern biotherapies employing antibodies are planned.