Chronic inflammatory bowel disease is included into autoimmune diseases, which is proved by presence of inflammatory lesions, circulating autoantibodies and the deposits of immune complexes in tissues. Coeliac disease (classic and atypical form), Crohn's Disease and ulcerative colitis are considered as chronic autoimmune bowel diseases. The auto-antibodies can be detected with indirect immunofluorescence, ELISA and immunoblotting methods. In coeliac disease the autoantibodies against endomysium (tissue transglutaminase) and antibodies against gliadin are found in patient's sera. The auto-antibody detecting is helpful in establishing diagnosis, controlling gluten-free diet effectiveness and during gluten challenge. In Crohn's disease and ulcerative colitis immunological laboratory tests are helpful to confirm the clinical diagnosis. The following auto-antibodies are tested: against cytoplasm of exocrinal pancreatic cells, and products of these cells, against the neutrophile cytoplasm and against goblet cells. The antibodies against Saccharomyces cerevisiae are also investigated. The clinical relevance of above autoantibodies is not clear, but it is suggested that their presence correlates with exacerbations and severe clinical outcome. In the present study the pictures of autoantibodies from fluorescent microscope were shown.