Eukaryotic cell function and survival rely on the use of a mitochondrial H+ electrochemical gradient (?p), which is composed of an inner mitochondrial membrane (IMM) potential (??mt) and a pH gradient (?pH). So far, ??mt has been assumed to be composed exclusively of H+. Using a rainbow of mitochondrial and nuclear genetic models, we have discovered that a Na+ gradient equates with the H+ gradient and controls half of ??mt in coupled-respiring mammalian mitochondria. This parallelism is controlled by the activity of the long-sought Na+-specific Na+/H+ exchanger (mNHE), which we have identified as the P-module of complex I (CI). Deregulation of this mNHE function, without affecting the canonical enzymatic activity or the assembly of CI, occurs in Leber's hereditary optic neuropathy (LHON), which has profound consequences in ??mt and mitochondrial Ca2+ homeostasis and explains the previously unknown molecular pathogenesis of this neurodegenerative disease.