We aimed to evaluate the transcription and translation of genes for uncoupling protein 2 (UCP2) & uncoupling protein 3 (UCP3) in rat heart mitochondria of both ventricles after myocardial ischemia followed by various periods of reperfusion. Seven groups of 8 male Wistar rats were evaluated for the effects of ischemia and also reperfusion, using Western blot of isolated mitochondrial proteins in addition to RNA extraction followed by real-time RT-PCR analysis. In rats with 30 min of reperfusion (R30) UCP2 protein was increased 213±33%, which is meaningfully more than the control group (P<0.001). Western blot showed increase in UCP2 protein level in groups receiving reperfusion for 60 min (R60), 120 min (R120) and 180 min (R180) as much as 152±28% (P<0.001 vs. control), 123±19% (P<0.01 vs. control) and 131±30% (P<0.01 vs. control), respectively. There was no statistically important difference in UCP2 mRNA between either right or left ventricles of ischemic and ischemia-reperfusion (IR) groups vs. control group. In the groups R180 and R240, UCP3 protein levels showed 131±27% and 102±18% increase, respectively (both P<0.001 vs. control group). However, the change in UCP3 level in other groups was not significantly different from the control group. UCP2 and UCP3 protein levels are considerably increased in the ischemic area early after acute myocardial IR. The right ventricular UCP2 protein expression does not change, that is, effect of IR on UCP2 protein is a local process. However, UCP3 protein level increased both in ischemic area of the left ventricle and in non-ischemic area of the right ventricle. Copyright © 2014 Elsevier Inc. All rights reserved.