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Autoimmune diseases may affect all parts of the gastrointestinal system and the liver. Autoantibodies can be very helpful in the diagnosis of these diseases. For detection, two main diagnostic techniques are available: indirect immunofluorescence technique (IFT) as well as solid phase assays as e. g. ELISA or immunoblot. Depending on symptoms and differential diagnosis, IFT may serve as screening assay and solid phase assays may serve as confirmatory assays. The esophagus can sometimes be affected by systemic autoimmune diseases; diagnosis is often facilitated by the proof of circulating autoantibodies. Atrophic gastritis is the most prominent autoimmune disease of the stomach also displaying circulating autoantibodies. Antibody diagnosis for celiac disease has been implemented in all common guidelines. For liver and pancreatic autoimmune diseases, there is a solid history for the significance of the detection of circulating autoantibodies. Knowledge of available tests and accurate implementation accelerates correct diagnosis in many cases., Competing Interests: Die Autorinnen/Autoren geben an, dass kein Interessenkonflikt besteht., (Thieme. All rights reserved.)