There are several different diseases in gastroenterology with an important role of immunological mechanisms in their pathogenesis. We know autoimmune diseases with immunological reactions against liver or pancreatic tissue. In addition there are diseases like chronic inflammatory bowel diseases representing inappropriate immunological reactions followed by inflammation and tissue destruction. The research of the last decade has contributed significantly to the understanding of the pathogenesis of diseases based on immunological mechanisms and consequently to the development of novel therapeutic strategies targeting molecules. Chronic inflammatory bowel diseases, autoimmune hepatitis, primary sclerosing cholangitis, primary biliary cirrhosis, autoimmune pancreatitis, and celiac disease are the most important diseases with immunological pathogenesis in Gastroenterology. Especially in chronic inflammatory bowel diseases ulcerative colitis and Crohn's disease with immunosuppressive drugs and monoclonal antibodies new preparations are used in therapy. Autoimmune pancreatitis was characterized as an own entity in the last years. Therefore, this review will focus on these diseases.