Defensins are endogenous antibiotics with broad microbicidal activity. A disturbed antimicrobial defense, as provided by Paneth and other epithelial defensins, seems to be a critical factor in the pathogenesis of inflammatory bowel diseases. Conspicuously, there is a relative lack of Paneth-cell alpha-defensins in ileal Crohn's disease (CD), both in the absence of a pattern recognition receptor nucleotide-binding oligomerization domain 2 (NOD2) frameshift mutation and, even more pronounced, in its presence. This deficit is independent of concurrent active inflammation and cannot be seen in active small intestinal ulcerative colitis (UC; pouchitis) as well as NOD2 wild-type graft vs. host ileitis. After intestinal transplantation, in case of NOD2 mutation, defensins are decreased before the onset of inflammation. In the majority of patients, the Paneth-cell deficiency is mediated by Wnt-TCF4, which suggests a disturbed Paneth-cell differentiation. In contrast, colonic CD is characterized by an impaired induction of mucosal beta-defensins, partly because of a low copy number of the beta-defensin gene cluster. In both ileal and colonic CD, the lack in defensins results in a broadly diminished antibacterial killing by the mucosa, which can also be found independent of inflammation. In summary, the main disease locations can be linked to distinct mechanisms of epithelial barrier dysfunction.