NOD2 variants have been identified to be a susceptibility factor for Crohn's disease. The NOD2 protein is an intracellular sensor of the bacterial wall product muramyl dipeptide (MDP) and activates the transcription factor NF-kappaB upon MDP-binding. NOD2 variants are associated with reduced NF-kappaB activation and reduced production of epithelial derived antibacterial peptides such as defensins. A reduced expression of defensins is described and found in patients with Crohn's disease and ulcerative colitis especially when NOD2 variants are present. Furthermore recent evidence from mouse models suggests that the ability of intestinal epithelial cells to activate NF-kappaB upon bacterial stimulation protects from mucosal inflammation. Taken together these data indicate that NOD2 mediated NF-kappaB activation, subsequent induction of anti-microbial peptides such as defensins and induction of cytokine expression are essential for the function of the intestinal barrier and for the prevention of bacterial translocation. The data indicate why a defect in the induction of this acute defense response is associated with chronic inflammation. Invading bacteria that cannot be readily detected and eliminated may start a backup mechanism of inflammation finally resulting in chronic inflammatory reaction followed by further impairment of the mucosal barrier.