Bovine heart submitochondrial particle transhydrogenase is inhibited by cations in a concentration and pH-dependent manner, and non-energy-linked transhydrogenation is inhibited to a greater extent by metals than the energy-linked reaction. The inhibition of the enzyme by Mg2+ is competitive with the NADP substrate and non-competitive with the NAD substrate. Mg2+ stimulates inactivation of the enzyme by 5,5'-dithiobis(2-nitrobenzoic acid), and protects against thermal and proteolytic inactivation. This suggests that Mg2+ binding in the NADP site alters transhydrogenase to a more thermostable conformation, which is less susceptible to attack by trypsin and more reactive with 5,5'-dithiobis(2-nitrobenzoic acid). Other cation inhibitors mimic Mg2+ in these properties. The order of effectiveness of the inhibitors tested is La3+ greater than Mn2+ greater than Ca2+ congruent to Mg2+ greater than Sr2+ greater than Na+ congruent to K+. This order is described by the Irving-Williams order for the stability of metal-ligand complexes, suggesting that carboxylates or amines may comprise the inhibitory cation binding site.