Autophagy associated genes have been identified as susceptible loci for inflammatory bowel disease. We investigated the role of a core autophagy factor, Atg5, in the development of dextran sodium sulfate (DSS) induced colitis. Intestinal epithelial cell (IEC) specific Atg5 gene deficient mice (Atg5 ΔIEC mice) were generated by cross of Atg5 floxed mice (Atg5 fl/fl) with transgenic mice expressing Cre recombinase driven by the villin promotor. Mice were given three cycles of 1.5% DSS in drinking water for 5 days and regular water for 14 days over a 60 day period. The dysfunc tion of autophagy characterized by a marked accumulation of p62 protein, a substrate for autophagy degradation, was detected in epithelial cells in the non inflamed and inflamed mucosa of inflammatory bowel disease patients. DSS colitis was exacerbated in Atg5 ΔIEC mice compared to control Atg5 fl/fl mice. Phosphorylation of inositol requiring transmembrane kinase/endonuclease1α (IRE1α), a sensor for endoplasmic reticulum stress, and c Jun N terminal kinase, a downstream target of IRE1α, were significantly enhanced in IECs in DSS treated Atg5 ΔIEC mice. Accumulation of phosphorylated IRE1α was enhanced by the treatment with chloroquine, an autophagy inhibitor. Apoptotic IECs were more abundant in DSS treated Atg5 ΔIEC mice. These findings suggest that Atg5 suppresses endoplasmic reticulum stress induced apoptosis of IECs via the degradation of excess p IRE1α.