This study tested the hypothesis that classic ischemic preconditioning can cause changes in gene expression patterns in the rabbit heart, assessed by gene array technology. Open-chest rabbits were randomly assigned to sham-operated and ischemically preconditioned groups. The sham-operated group received 5 hours and 20 minutes of no intervention, while the ischemically preconditioned group was subjected to two episodes of preconditioning ischemia (5 minutes each) separated by 5 minutes of reperfusion, followed by an additional 5 hours and 5 minutes of reperfusion. (33)P-labeled cDNA from the sham-operated hearts and the nonischemic and preconditioned areas of the ischemically preconditioned group was hybridized to filters spotted with 18,376 human cDNA clones. Altogether, 35 genes with significantly altered expression patterns were discovered. In the preconditioned area, genes for MAPKAP kinase 3 and cathepsin G were up-regulated. In the nonischemic area, genes for GTP exchange factor, Na(+), K(+)-ATPase, Zn finger protein 35, a representative of the CEA family, cytochrome c oxidase, mitogen-responsive phosphoprotein, and Ran-binding protein were up-regulated. None of the identified genes had been previously reported to be involved in ischemic preconditioning.