Available methods to measure mitochondrial [Ca2+] (1Ca(2+)](M)) include both targeted proteins and fluorescent dyes. Targeted proteins usually report much higher [Ca2+](M) values than fluorescent dyes, up to two orders of magnitude. However, we show here that the low-Ca2+-affinity dye rhod-5N provides [Ca2+](M) values similar to those reported by targeted aequorin, suggesting that the discrepancies are mainly due to the higher Ca2+-affinity of the fluorescent dyes used. We find rhod-5N has an apparent in situ intramitochondrial Kd around 0.5 mM. Addition of Ca2+ buffers containing between 4.5 and 10 mu M [Ca2+]to permeabilized cells loaded with rhod-5N induced increases in calibrated [Ca2+](M) up to the 100 mu M-1 mM range, which were dependent on mitochondrial membrane potential. Ca2+ release from mitochondria was largely dependent on [Na+]. We have then used rhod-5N loaded cells to investigate the [Ca2+](M) response to agonist stimulation at the single-cell and subcellular level. The [Ca2+](M) peaks induced by histamine varied by nearly 10-fold among different cells, with a mean about 25 mu M. In the presence of the Ca2+ uniporter stimulator kaempferol, the [Ca2+](M) peaks induced by histamine were also highly variable, and the mean [Ca2+](M) peak was 3-fold higher. Simultaneous measurement of cytosolic and mitochondrial [Ca2+]peaks showed little correlation among the heights of the peaks in both compartments. Studying the [Ca2+](M) peaks at the subcellular level, we found significant heterogeneities among regions in the same cell. In particular, the [Ca2+](M) increase in mitochondrial regions close to the nucleus was more than double that of mitochondrial regions far from the nucleus. (C) 2011 Elsevier Ltd. All rights reserved.