The Na + -Ca 2+ exchanger (NCX) is involved in the regulation of Ca 2+ concentration in the myocardium. The plasmalemmal NCX basically functions in the forward (transplasmalemmal Ca 2+ efflux) mode, but under pathological conditions such as ischemia, it is postulated to function in the reverse (Ca 2+ influx) mode and contribute to cellular damage. 1) SEA0400 (2-[4-[(2,5-difluorophenyl)methoxy]phenoxy]-5-ethoxyaniline) is a selective inhibitor of NCX with minimum effects on other plasmalemmal transporters and ion channels, [2][3][4][5] and thus have been used as a potent pharmacological tool in NCX research. We have previously examined the effects of SEA0400 on a coronary-perfused myocardial ischemia-reperfusion model and found that SEA0400 enhances the recovery of contractile force and action potential duration after reperfusion. 6) SEA0400 attenuated cytoplasmic and mitochondrial Ca 2+ overload and preserved tissue ATP content and mitochondrial membrane potential during ischemia. 7) These results suggested that inhibition of plasmalemmal NCX protects the mitochondria through attenuation of Ca 2+ overload during myocardial ischemia. However, the following issues relevant to this hypothesis have not yet been clarified. Firstly, can the attenuation of the rise in mitochondrial Ca 2+ be attributed to the attenuation of the rise in cytoplasmic Ca 2+ by SEA0400? Secondly, can the preservation of the mitochondrial membrane potential be attributed to the attenuation of the rise in mitochondrial Ca 2+ by SEA0400? Thirdly, does SEA0400 have any direct effect on mitochondrial Ca 2+ transport pathways including the mitochondrial NCX, which has been considered to have pivotal roles in intracellular Ca 2+ handling? 8) In the present study, to obtain information to answer these questions, we constructed a fluorescence-based system for the analysis of mitochondrial Ca 2+ concentration. We used the rat embryonic heart derived H9c2 cells expressing the mitochondria-targeted yellow cameleon 3.1, a protein Ca 2+ indicator based on fluorescence resonance energy transfer (FRET) between cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP). 9) After permeabilizing the cells with digitonin, the extramitochondrial environment could be manipulated by changing the cell perfusate and the resulting changes in mitochondrial Ca 2+ concentration monitored with yellow cameleon fluorescence ratio. We studied the regulation of mitochondrial Ca 2+ under normal and ischemic condition, and examined the effect of pharmacological agents including SEA0400.