Composition and amount of 45Ca2+-binding proteins in the inner membrane fraction of rat liver and Zajdela hepatoma mitochondria were determined. In the inner membrane of liver mitochondria, three major 45Ca2+-binding polypeptides: a protein of approximately 130 kDa (carbamoyl-phosphate synthetase), a glycoprotein of 43-44 kDa (previously considered as the calcium uniporter), and 29-30 kDa protein were found. These components were absent (130 kDa component) or relatively reduced (43-44 kDa and 29-30 kDa components) in the inner membrane of hepatoma mitochondria. Previously unknown low molecular mass polypeptides, having very high Ca2+-binding ability, were found in the inner membrane of hepatoma mitochondria. One of them might be the natural Ca2+-binding inhibitor of H+-ATPase.