In the present study, we employed rat intestinal epithelial cell line (IEC-6) in vitro to investigate the effects of heat stress on cell injury and apoptosis. IEC-6 cells were assigned to two groups as follows: Control group (strictly regulated at 37 degrees C), Heat stress group (exposed to 42 degrees C for 4 hours). Changes in cell morphology following heat treatment were observed using a phase-contrast inverted biological microscope. The permeability was determined using a fluorescence microscope after staining with acridine orange (AO) and propidium iodide (PI). Cell viability was measured using an MTT assay, and apoptosis was determined using FACS analysis. The expression of genes related to apoptosis (including bax, bcl-2 and caspase-3) was measured by RT-PCR. Results show that morphological damage was obvious, cell permeability was significantly elevated, apoptosis was significantly increased, and the expression of bax and caspase-3 was significantly increased while bcl-2 was decreased following heat treatment. In conclusion, our results show that heat stress induces damage and apoptosis in rat intestinal epithelial cell via regulated the gene expression of bax, caspase-3 and bcl-2.