The complete amino acid sequence of mitochondrial malate dehydrogenase from rat heart has been determined by chemical methods. Peptides used in this study were purified after digestions with cyanogen bromide, trypsin, endoproteinase Lys C, and staphylococcal protease V-8. The amino acid sequence of this mature enzyme is compared with that of the precursor form, which includes the primary structure of the transit peptide. The transit peptide is required for incorporation into mitochondria and appears to be homologous to the NH2-terminal arm of a related cytoplasmic enzyme, pig heart lactate dehydrogenase. The amino acid differences between the rat heart and pig heart mitochondrial malate dehydrogenases are analyzed in terms of the three-dimensional structure of the latter. Only 12/314 differences are found; most are conservative changes, and all are on or near the surface of the enzyme. We propose that the transit peptide is located on the surface of the mitochondrial malate dehydrogenase precursor.