This paper reports an investigation on the regulation of the mitochondrial cyclosporin A-sensitive permeability transition pore (MTP). Energized, coupled rat liver mitochondria incubated in sucrose medium in the presence of phosphate maintain a high proton electrochemical gradient (delta microH) and a low permeability to solutes. Addition of a small (10-20 microM) Ca2+ pulse leads to a transient membrane depolarization. After Ca2+ accumulation, a high delta microH is recovered, and mitochondria remain coupled indefinitely. Yet, addition of fully uncoupling concentrations of carbonyl cyanide-p-trifluoromethoxyphenyl hydrazone (FCCP) brings about MTP opening within seconds. This finding confirms that MTP opening is the consequence rather than the cause of membrane depolarization, and allowed us to study the operation of the MTP in a synchronized population of mitochondria, since pore opening can be triggered by the addition of uncoupler under a series of experimental conditions. We find that three regulatory sites can be defined: (i) an internal Me2+ binding site: when this site is occupied by Ca2+, the pore "open" probability increases, while other Me2+ ions (Sr2+, Mn2+) have an inhibitory effect; (ii) an external Me2+ binding site: when this site is occupied by Me2+ ions, including Ca2+, the pore open probability decreases; (iii) an independent cyclosporin A binding site: when this site is occupied by cyclosporin A the pore open probability decreases. We show that at variance from the case of cyclosporin A, MTP inhibition by the phospholipase A2 inhibitors nupercaine and trifluoperazine is Ca(2+)-competitive and is presumably related to interference by these drugs with Ca2+ binding to the internal regulatory site.