Despite many years of intensive research the pathogenesis of inflammatory bowel diseases is still enigmatic. All efforts to identify the cause of Crohn's disease and ulcerative colitis in a dysregulation of specific immune mechanisms have failed. This review presents a novel pathogenetic concept, based on the expression of natural mucosal antibiotic peptides. These so called defensins are part of innate immunity and defend the mucosa as antimicrobial peptides against intraluminal potentially pathogenic and invasive bacteria. In contrast to ulcerative colitis, Crohn's disease is characterised by a diminished defensin expression. This defect may represent the molecular pathogenesis of this disease.