Reports about the effect of ischemia and reperfusion on specific activities of the respiratory chain are often discrepant. One of the factors that govern this discrepancy is that typical mechanical procedures for mitochondrial isolation yield largely sub-sarcolemmal mitochondria (SSM), while the interfibrillar mitochondria (IFM), which provide most of the energy for the contractile apparatus, are under-represented. Here we investigated the impact of myocardial ischemia and reperfusion on SSM and IFM separately. Thirty-two Wister rats were randomly divided into four groups: control groups, ischemia groups, reperfusion groups and precondition groups. SSM and IFM were isolated from the rats' hearts from all the groups. The mitochondrial membrane potential (Delta psi) and swelling were assessed at energized (using either 5 mM succinate or 5 mM glutamate and 5 mM malate (GM) as a substrate) and non-energized conditions, where IFM showed better resistance to change in both conditions. Results showed that IFM have a higher coupling efficiency than SSM when energized by GM, but lower than SSM when energized with succinate. Preconditioning the rats' hearts prior to ischemia or reperfusion preserved the physiological and biochemical functions of both IFM and SSM and are energy dependent. The distinct physiological-biochemical functions of the mitochondrial sub-populations during ischemia and reperfusion depend on the overall energy status of the mitochondrial sub-population. (C) 2012 Elsevier Inc. All rights reserved.