Coenzyme Q10 (CoQ10) has been extensively studied as adjunctive therapy for ischemic heart disease, and its cardioprotective ability is well-established. The mitochondrial respiratory chain contains several coenzymes, including CoQ1, CoQ2, CoQ4, CoQ6, CoQ7, CoQ8, CoQ9, and CoQ10. It is not known whether other CoQs, especially CoQ9, is equally cardioprotective as CoQ10. The present study was designed to determine if CoQ 9 could protect guinea pig hearts from ischemia reperfusion injury. Guinea pigs were randomly divided into three groups: groups I and II were fed CoQ 9 and CoQ10, respectively, for 30 days while group III served as control. After 30 days, the guinea pigs were sacrificed and isolated hearts were perfused via working mode were subjected to 30 min ischemia followed by 2 h of reperfusion. Cardioprotection was assessed by evaluating left ventricular function, ventricular arrhythmias, myocardial infarct size, and cardiomyocyte apoptosis. Samples of hearts were examined for the presence of CoQ9 and CoQ10. The results demonstrated that both CoQ9 and CoQ10 were equally cardioprotective, as evidenced by their abilities to improve left ventricular performance and to reduce myocardial infarct size and cardiomyocyte apoptosis. High performance liquid chromatographic (HPLC) analysis revealed that a substantial portion of CoQ9 had been converted into CoQ10. The results indicate that CoQ9 by itself, or after being converted into CoQ10, reduced myocardial ischemia/reperfusion-induced injury.