Ruthenium red is a well-known and effective inhibitor of the mitochondrial Ca2+ uniporter; however, Reed and Bygrave [(1974) FEBS Lett. 46, 109-114] tentatively attributed this inhibition to a colorless impurity present in commercial samples of ruthenium red (RR). This component has now been isolated and a derivative, (mu-O) [(HCO2)(NH3)4Ru]2Cl3, structurally characterized. The active species in solution appears to be the symmetrical oxo-bridged ion, [X(NH3)4Ru-O-Ru(NH3)4X]3+, where X = Cl- or OH-. Its absorption spectrum shows a maximum at 360 nm. The dinuclear ruthenium ammine complex inhibits Ca(2+)-stimulated respiration of rat liver mitochondria with an I50 of 3.5 pmol/mg of protein compared to the value of 60 pmol of RR/mg of protein. The inhibition by the dinuclear compound is noncompetitive with Ca2+. Respiration-linked swelling of mitochondria induced by Cd2+ also responds similarly to both the dinuclear complex and RR. A close correlation was observed between binding to mitochondria as monitored with 103Ru-labeled dinuclear complex and inhibition of Ca2+ transport. A Scatchard plot yielded estimates of maximum specific binding and dissociation constant of 7.5 pmol/mg of protein and 1.3 nM, respectively. The inhibitor has the characteristics of a satisfactory affinity ligand for purification of the uniporter.