Abstract Stobadine (ST), a novel drug with pyridoindol structure, was recently found to prevent reperfusion injury in rat brain. The aim of the present study was to reveal whether ST may prevent peroxidative changes in the heart and brain that were triggered by postischemic reperfusion of the brain. In the brain, reperfusion significantly increased the contents of malondialdehyde (MDA) by 43.8 % and conjugated diens (CD) by 24.5% when compared with the end of ischemia. In the heart, contents of MDA and CD in reperfusion became elevated three fold and by 41.7 %, respectively, when comparing to the values at the end of ischemia. In the heart, no significant changes in activities of the superoxide dismutase (SOD) and glutathione peroxidase (GPx) induced by ischemia or reperfusion were detected. In contrast, reperfusion induced a slight decrease in GPx activity in the brain. In accordance with our previous results, an application of ST (2 mg/kg) to the femoral artery shortly prior to reperfusion of the ischemic brain, prevented significantly MDA and CD accumulation in brain. Nevertheless, ST was not able to prevent the brain-ischemia/reperfusion-induced elevation of MDA and CD contents in the heart.