a b s t r a c tAvailable methods to measure mitochondrial [Ca 2+ ] ([Ca 2+ ] M ) include both targeted proteins and fluorescent dyes. Targeted proteins usually report much higher [Ca 2+ ] M values than fluorescent dyes, up to two orders of magnitude. However, we show here that the low-Ca 2+ -affinity dye rhod-5N provides [Ca 2+ ] M values similar to those reported by targeted aequorin, suggesting that the discrepancies are mainly due to the higher Ca 2+ -affinity of the fluorescent dyes used. We find rhod-5N has an apparent in situ intramitochondrial Kd around 0.5 mM. Addition of Ca 2+ buffers containing between 4.5 and 10 M [Ca 2+ ] to permeabilized cells loaded with rhod-5N induced increases in calibrated [Ca 2+ ] M up to the 100 M-1 mM range, which were dependent on mitochondrial membrane potential. Ca 2+ release from mitochondria was largely dependent on [Na + ]. We have then used rhod-5N loaded cells to investigate the [Ca 2+ ] M response to agonist stimulation at the single-cell and subcellular level.The [Ca 2+ ] M peaks induced by histamine varied by nearly 10-fold among different cells, with a mean about 25 M. In the presence of the Ca 2+ uniporter stimulator kaempferol, the [Ca 2+ ] M peaks induced by histamine were also highly variable, and the mean [Ca 2+ ] M peak was 3-fold higher. Simultaneous measurement of cytosolic and mitochondrial [Ca 2+ ] peaks showed little correlation among the heights of the peaks in both compartments. Studying the [Ca 2+ ] M peaks at the subcellular level, we found significant heterogeneities among regions in the same cell. In particular, the [Ca 2+ ] M increase in mitochondrial regions close to the nucleus was more than double that of mitochondrial regions far from the nucleus.