Ischemic preconditioning (IPC) is a phenomenon where heart is rendered more resistant to subsequent ischemia-reperfusion (I-R)-induced injury by one or more brief episodes of I-R. The mechanisms responsible for cardio-protective effects of IPC are not well characterized. The objective of the study was to characterize gene expression profiles in the left ventricle of male Wistar rat hearts exposed to I-R or IPC followed by I-R. Group I included hearts that were only perfused for 30 min. Group 2 included hearts that underwent 30 min perfusion followed by 40 min I and 30 min R. Group 3 comprised 30 min perfused hearts that were subjected to IPC (5 min I + 10 min R + 5 min I + 10 min R) followed by I-R. Total RNAs were isolated from left ventricular tissues. Codelink gene expression system (GE Healthcare) was used for cRNA target preparation, hybridization of microarrays (Rat UmSet 10K CodeLink bioarrays, GE Healthcare) and detection. Microarrays were scanned with Affymetrix 428 Array scanner. Data analyses were carried out with GeneSifter rnicroarray data analysis software. We determined a total of 140 transcripts (>= 2-fold change) whose expressions were changed (44 up-regulated and 96 down-regulated) accompanying to I-R injury compared to perfused only hearts. Twenty-three transcripts including Ryr3, Crk, Dio1, Npy1r, Ptpra, Cyp51 that were down-regulated by I-R injury, were up-regulated by cardiac IPC. IPC down-regulated the expression of several transcripts including Atf3 (activating transcription factor 3), carboxypeptidase A1 (Cpa 1), Slc38a4, Blk which were up-regulated by I-R. In conclusion, evaluation of global gene expression profiling via microarray-based technologies provides a molecular portrait of cardiac IPC of the left ventricular tissue of rat heart. Copyright C 2007 John Wiley & Sons, Ltd.