Aim To test the changes of gene expression profiles after myocardical ischemic preconditioning in rats. Methods The changes of gene expression profiles of 4 096 genes in rat hearts were observed using cDNA chip and the significance of the changes in gene expression was analyzed. Results The expression of 48 genes was up regulated and 27 genes was down regulated after ischemic preconditioning. The changes in gene expression were further confirmed by RT PCR. The significance of the changes of gene expression profiles in the myocardial protection induced by ischemic preconditioning was analyzed. Conclusions Ischemic preconditioning resulted in the changes of myocardical gene expression profiles. The results were helpful to elucidate the molecular mechanism of myocardial protection induced by ischemic preconditioning and provided new clues for prevention and treatment of myocardial ischemia reperfusion injury and ischemic heart diseases.