Inflammatory bowel disease involves a break of tolerance to the commensal microbiota. Aberrations in the mucosal IgA system may, therefore, be part of the inflammatory bowel disease pathogenesis. In gluten-induced enteropathy, however, it has been suggested that a mucosal IgA response may promote the progression of celiac disease and dermatitis herpetiformis by enhancing the uptake of gluten peptides and inhibiting the enzyme activity of tissue transglutaminase. A mucosal IgA response may also promote gastritis by protecting Helicobacter pylori from complement attack. In food allergy, several facets of the epithelial barrier function may show deficiency, including secretory IgA.