Initial differentiation between irritable bowel syndrome and CIBD can be achieved by non-invasive antigen detection of calprotectin in stool and thus provide a decisive precharacterisation of bowel-associated inflammation (see chapter Calprotectin). Alongside the single IIF tests, the high diagnostic demands on differentiated CIBD diagnostics are also met by various highly specific mosaics (CIBD profiles) specifically developed for serological diagnostics of the autoimmune intestinal diseases CD and UC.

Autoantibodies against the exocrine pancreas are a reliable marker for CD. They have a high disease-specific significance due to their organ specificity, disease association and frequently high serum concentration. Due to the fact that the inflammation of the intestinal wall in CD is caused by the autoantigens contained in the pancreas secretion, particularly the proteoglycans CUZD1 and GP2, the determination of autoantibodies against the pancreas antigens rPAg1 (CUZD1) and/or PAg2 (GP2) using IIFT represents a new dimension in serological CD diagnostics. Antibodies against Saccharomyces cerevisiae (ASCA) enrich the serodiagnostics for CD by a further specific parameter.

Autoantibodies against intestinal goblet cells, which occur exclusively in UC, are pathognomonic markers for this autoimmune disease. The target antigen responsible for UC has not yet been exactly identified. The serological determination of autoantibodies against DNA-bound lactoferrin contributes significantly to the diagnosis of CIBD, particularly of UC.