NADH:ubiquinone oxidoreductase (complex I) is a major source of reactive oxygen species in mitochondria and a significant contributor to cellular oxidative stress. Here, we describe the kinetic and molecular mechanism of superoxide production by complex I isolated from bovine heart mitochondria and confirm that it produces predominantly superoxide, not hydrogen peroxide. Redox titrations and electron paramagnetic resonance spectroscopy exclude the iron-sulfur clusters and flavin radical as the source of superoxide, and, in the absence of a proton motive force, superoxide formation is not enhanced during turnover. Therefore, superoxide is formed by the transfer of one electron from fully reduced flavin to O2. The resulting flavin radical is unstable, so the remaining electron is probably redistributed to the iron-sulfur centers. The rate of superoxide production is determined by a bimolecular reaction between O2 and reduced flavin in an empty active site. The proportion of the flavin that is thus competent for reaction is set by a preequilibrium, determined by the dissociation constants of NADH and NAD ؉ , and the reduction potentials of the flavin and NAD ؉ . Consequently, the ratio and concentrations of NADH and NAD ؉ determine the rate of superoxide formation. This result clearly links our mechanism for the isolated enzyme to studies on intact mitochondria, in which superoxide production is enhanced when the NAD ؉ pool is reduced. Therefore, our mechanism forms a foundation for formulating causative connections between complex I defects and pathological effects.flavin ͉ iron-sulfur cluster ͉ semiquinone ͉ oxidative stress T he production of reactive oxygen species, such as superoxide, by mitochondria is a major cause of cellular oxidative stress. It contributes to many pathological conditions such as Parkinson's and other neurodegenerative diseases, ischemia reperfusion injury, atherosclerosis, and aging (1-3). In mammalian mitochondria, most of the superoxide originates from NADH:ubiquinone oxidoreductase (complex I) and ubiquinol: cytochrome c oxidoreductase (complex III) of the electron transport chain, but there is increasing evidence that superoxide production by complex I, into the mitochondrial matrix, is predominant (4, 5). Indeed, complex I deficiencies have been identified across a wide spectrum of pathologies and linked to enhanced superoxide production as well as to deficiencies in energy production (6-10). Therefore, it is imperative to define how, why, and when superoxide is produced by complex I to formulate causative connections with pathological effects and rational proposals for how defects may be addressed.Many previous studies have addressed the question of how superoxide is produced by complex I (11-18). Most of these studies examined intact mitochondria or submitochondrial particles, in which it is difficult to correlate observations directly to complex I, or to define and control the conditions precisely (NADH, NAD ϩ , ubiquinone, and ubiquinol concentrations, redox status, proton motive...