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 1 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 UniSet 10 K CodeLink bioarrays, GE Healthcare) and detection. Microarrays were scanned with Affymetrix 428 Array scanner. Data analyses were carried out with GeneSifter microarray 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 (Cpa1), 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 © 2007 John Wiley & Sons, Ltd.