Previous studies indicated that eosinophils and mast cells accumulate and become activated in inflammatory bowel disorders. The aim of the study was to examine the presence of eosinophil and mast cell mediators in human stool samples of patients with inflammatory bowel disorders. We measured eosinophil cationic protein (ECP), eosinophil protein X (EPX), methylhistamine, and alpha 1-antitrypsin in fecal samples of 136 patients (62 Crohn's disease, 24 ulcerative colitis, 15 intestinal food allergy, 35 other gastrointestinal diseases) and 8 healthy controls. We found strongly elevated levels of ECP (median: 29, range: 0.4-1783 ng/g feces) and EPX (803, 10-33,225 ng/g) in all patients groups compared to controls (ECP: 1.5, 0.5-55 ng/g; EPX: 235, 12-746 ng/g). Similar results, albeit less pronounced, were obtained for methylhistamine and alpha 1-antitrypsin. Particularly high concentrations of ECP and EPX were found in patients with active mucosal inflammation. In conclusion, the study presents an easy and reliable method for the detection of fecal ECP, EPX, and methylhistamine and may provide a tool to gain insight into the pathogenesis of inflammatory bowel diseases and have potential as diagnostic test.