Abstract The processes affecting myocardial survival in ischemia were studied in perfused rat hearts by using largely non-invasive methods based on optical monitoring and nuclear magnetic resonance (NMR). Ischemic preconditioning (IPC) has been shown to protect the heart considerably from ischemic damage in all species studied. F1Fo-ATPase inhibition has been suggested to involve the mechanism of IPC, but its significance has been doubted, partly because ischemic inhibition of F1Fo-ATPase has been considered insignificant in rat. An improved method of F1Fo-ATPase activity measurement was used in which the time-consuming isolation of mitochondria was omitted and the salt concentration and pH conditions were optimized. It was demonstrated that ischemic F1Fo-ATPase inhibition does occur in rat, and that the method can also be applied in human myocardium. The mitochondrial ATP-sensitive potassium (mitKATP) channel opener, diazoxide, attenuated myocardial damage and enhanced ischemic inhibition of F1Fo-ATPase similar to IPC. All of these effects were abolished with the mitKATP inhibitor 5-HD. These results suggest that mitKATP opening is connected to F1Fo-ATPase inhibition in the mechanism of IPC. Observations of the nature of F1Fo-ATPase inhibition in isolated mitochondria suggest that IF1 binding is involved in the inhibition. Calcium perturbations in ischemia-reperfusion were studied in intact heart using calcium probing with Fura-2. It was found that compensation for tissue autofluorescence and pH changes were necessary for reliable Ca2+ monitoring. IPC significantly decreased myocardial calcium accumulation in ischemia, and magnesium quenching of cytosolic Fura-2 fluorescence showed that this is mainly mitochondrial. The attenuation of mitochondrial calcium overload was connected to an enhanced decrease in mitochondrial membrane potential in IPC. The role of calcium in respiratory control and in substrate selection was studied during fatty acid oxidation. The energy state evaluated by 31P-NMR decreased slightly during hexanoate infusion upon calcium-induced inotrophy, and a tendency for NADH and flavoprotein oxidation was also monitored. These observations are in agreement with the theory that mitochondrial respiration is mainly determined by the energy expenditure. Even a 50 μM octanoate concentration completely surpassed glucose and internal substrates as a preferential myocardial energy source. The fatty acid dominance remained unaltered even upon a calcium-induced increase in energy consumption evaluated by 13C-NMR. The rate of anaplerosis was found to be considerable during octanoate oxidation, and it was emphasised during low cardiac workload.