Abdominal pain and diarrhoea are common symptoms of conditions ranging from chronic inflammatory bowel disease to infections of the digestive tract, celiac disease or irritable bowel syndrome. Complete blood count and other inflammatory parameters in the blood are also not specific to inflammation localized in the intestines, so diagnoses of inflammatory bowel disease are often made with considerable delay. On the other hand, people with functional diseases, such as irritable bowel syndrome are often referred to painful and actually needless diagnostic procedures. Calprotectin in stool is an ideal marker for differentiation between intestinal inflammation and irritable bowel syndrome. Elevated levels of calprotectin in stool samples are found in cases of inflammatory bowel disease, infectious gastroenteritis, or colorectal carcinoma. For functional disorders like irritable bowel syndrome, and in celiac disease, calprotectin levels are within the normal range. The detection of fecal calprotectin is a simple, non-invasive test that can reasonably be carried out before any imaging or endoscopy, and thus helps to avoid unnecessary, painful and costly colonoscopies in patients with functional diarrhoea. The non-invasive calprotectin tests can easily be performed in children and pregnant women, with no adverse effects. Calprotectin concentrations correlate with disease activity in ulcerative colitis and Crohn’s disease. They decline with response to therapy, and increasing calprotectin levels may indicate relapses even before clinical symptoms become evident. Calprotectin in stool samples is an accurate early indicator for intestinal inflammation and is now available for Orgentec’s Alegria instrument with fully automated walk-away design. The Alegria system allows for rapid automated analysis of single samples and up to 30 tests in only 90 minutes. There are no limits for sample selection. Laboratory parameters from autoimmunity (e.g. if celiac disease is suspected) or infectious disease serology can be analysed simultaneously in one single automated Alegria test run.