99mTc-gluconate has previously been shown to bind to isolated rat heart mitochondria. In the presence of potassium cyanide this binding is enhanced several fold, an effect which has been shown to be correlated to the efficiency of the in vivo binding of the isotope complex in ischemic dog hearts. The present investigation shows that the potassium cyanide-induced binding was mainly localized to the mitochondrial inner membrane; in the presence of cyanide other organelles, e.g., nuclei and liver microsomes also showed some binding. Boiling, lipid extraction, or addition of N-ethylmaleimide caused a variable inhibition of the binding of 99mTc-gluconate to rat heart mitochondria, which also was markedly influenced by temperature, pH, time, and concentrations of protein and isotope complex, but not by conditions affecting energy levels or calcium transport. Fractionation of submitochondrial particles exposed to 99mTc-gluconate in the presence of potassium cyanide indicated that the 99mTc-gluconate-binding component cofractionated with cytochrome oxidase. It is postulated that a protein component localized in the mitochondrial inner membrane, possibly cytochrome oxidase, is responsible for the binding of 99mTc-gluconate.