Here, we describe two complementary assays designed to analyze mitochondrial Na(+)/Ca(2+) exchange activity. In both procedures, the counter ion transport of sodium and calcium ions across the inner membrane of mitochondria is assayed in permeabilized cells preloaded with a mitochondria-selective Na(+) probe, CoroNa-Red, or with a mitochondria-targeted calcium sensor, ratiometric-pericam, respectively. These methods, therefore, do not require a mitochondrial preisolation step, with the native cellular mitochondrial architecture being maintained. Importantly, these methods equilibrate the cytosol with the extracellular milieu to allow control over the extra-mitochondrial ionic environment, while eliminating any possible interference by plasma membrane transporters.