Paraquat (1,1-dimethyl-4,4-bipyridinium dichloride) is widely used as a redox cycler to stimulate superoxide production in organisms, cells, and mitochondria. This superoxide production causes extensive mitochondrial oxidative damage, however, there is considerable uncertainty over the mitochondrial sites of paraquat reduction and superoxide formation. Here we show that in yeast and mammalian mitochondria, superoxide production by paraquat occurs in the mitochondrial matrix, as inferred from manganese superoxide dismutase-sensitive mitochondrial DNA damage, as well as from superoxide assays in isolated mitochondria, which were unaffected by exogenous superoxide dismutase. This paraquat-induced superoxide production in the mitochondrial matrix required a membrane potential that was essential for paraquat uptake into mitochondria. This uptake was of the paraquat dication, not the radical monocation, and was carrier-mediated. Experiments with disrupted mitochondria showed that once in the matrix paraquat was principally reduced by complex I (mammals) or by NADPH dehydrogenases (yeast) to form the paraquat radical cation that then reacted with oxygen to form superoxide. Together this membrane potential-dependent uptake across the mitochondrial inner membrane and the subsequent rapid reduction to the paraquat radical cation explain the toxicity of paraquat to mitochondria.Paraquat (1,1Ј-dimethyl-4,4Ј-bipyridinium dichloride; PQ) 2 is used to increase superoxide (O 2 . ) flux when investigating oxidative stress (reviewed in Refs. 1 and 2). The paraquat dication (PQ 2ϩ ) accepts an electron from a reductant to form the paraquat monocation radical (PQ . . and regenerate PQ 2ϩ (Fig. 1A). This redox cycling is a proximal cause of PQ toxicity, as indicated by the protection against PQ by superoxide dismutase (SOD) overexpression or administration of SOD mimetics (4 -8), and by the PQ hypersensitivity caused by SOD deficiency (9 -11).PQ has been used to generate O 2 . in systems ranging from isolated mitochondria (12-15) and cultured mammalian cells (4,14,16,17), to whole organisms including Saccharomyces cerevisiae (18 -21), Caenorhabditis elegans (22, 23), Drosophila melanogaster (9, 24 -26), and rodents (6,11,27). In many of these studies, PQ increases mitochondrial oxidative damage; for example, mitochondrial expression of human peroxiredoxin 5 protects yeast more effectively against PQ toxicity than expression in the cytosol (19); flies overexpressing catalase in mitochondria are resistant to PQ, whereas enhancement of cytosolic catalase was not protective (24); RNA interference silencing of MnSOD (the isoform of superoxide dismutase located in the mitochondrial matrix) in flies causes hypersensitivity to PQ (9), mice heterozygous for MnSOD show greater sensitivity to PQ than wild-type (11), and mitochondrial swelling is one of the earliest ultrastructural changes upon PQ exposure in vivo (28,29). Therefore the interaction of PQ with mitochondria is an important component of its toxicity, and PQ is used in expe...