The development of targeted probes (based on the molecular engineering of luminescent or fluorescent proteins) has allowed the specific measurement of [Ca2+] in intracellular organelles or cytoplasmic subdomains. This approach gave novel information on different aspects of cellular Ca2+ homeostasis. Regarding mitochondria, it was possible to demonstrate that, upon physiological stimulation of cells, Ca2+ is rapidly accumulated in the matrix. We will discuss the basic characteristics of this process, its role in modulating physiological and pathological events, such as the regulation of aerobic metabolism and the induction of cell death, and new insight into the regulatory mechanisms operating in vivo.