Defect in intestinal epithelial structure is a critical etiological factor of several intestinal diseases such as inflammatory bowel disease. The objective of this study was to evaluate the effect of grape seed extract (GSE), which contains a mixture of polyphenols, on ileal mucosal structure and inflammation in interleukin (IL)-10-deficient mice, a common model for studying inflammatory bowel disease. Wild-type and IL-10-deficient mice were fed GSE at 0 or 1% (based on dry feed weight) for 16 weeks. GSE supplementation decreased crypt depth and increased (P < 0.05) the ratio of villus/crypt length in the terminal ileum. Consistently, the dietary GSE decreased (P < 0.05) proliferation and enhanced (P < 0.05) differentiation of epithelial cells. These changes in gut epithelium were associated with the suppression of nuclear factor kappa-light-chain-enhancer of activated B-cell (NF-κB) signaling. Furthermore, compared with WT mice, IL-10 deletion promoted beclin-1 and AMPK expression, both of which were decreased to normal by GSE supplementation. These changes were associated with alterations in epithelial barrier function as indicated by reduced pore forming claudin-2 protein expression and increased barrier forming claudin-1 protein expression in the ileum of GSE supplemented mice. In summary, our data indicates that GSE exerts protective effects to the ileal epithelial structure in IL-10-deficient mice possibly through the suppression of inflammatory response.