We investigated the mechanisms underlying damage to rat small intestine in heat-and shake-induced stress.Eighteen Sprague-Dawley rats were randomly divided into a control group and a 3—day stressed group treated 2 h daily for 3 days on a rotary platform at 35℃ and 60 r/ min.Hematoxylin and eosin-stained paraffin sections of the jejunum following stress revealed shedding of the villus tip epithelial cells and lamina propria exposure.Apoptosis increased at the villus tip and extended to the basement membrane.Photomicrographs revealed that the microvilli were shorter and sparser; the nuclear envelope invaginated and gaps in the karyolemma increased; and the endoplasmic reticulum (ER) swelled significantly.Gene microarray analysis assessed 93 differentially expressed genes associated with apoptosis, ER stress, and autophagy.Relevant genes were compiled from the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases.Forty-one genes were involved in the regulation of apoptosis, fifteen were related to autophagy, and eleven responded to ER stress.According to KEGG,the apoptosis pathways, MAPK signaling pathway, mTOR signaling pathway, and regulation of autophagy may have been activated.Casp3, Casp12, andLC3 increased significantly at the villus tip while mTOR decreased; phosphorylated-AKT (P—AKT) decreased.ER stress was involved and induced autophagy and apoptosis in rat intestinal damage following heat and shake stress.Bioinformatic analysis will help determine the underlying mechanisms in stress-induced damage in the small intestine.