Faecal calprotectin is a biomarker for inflammation in the intestinal mucosa. Faecal calprotectin has the ability to detect inflammatory causes of gastrointestinal symptoms and to distinguish these from irritable bowel syndrome. The test is very sensitive but not specific to any particular gastrointestinal disease. In inflammatory bowel disease, faecal calprotectin correlates with symptoms, biochemical markers and the endoscopic findings. It can be used to monitor disease activity, treatment response and mucosal healing as well as predict relapse. We propose an algorithm for the use of faecal calprotectin in patients with unspecific abdominal complaints.