Selective activation of mitoK(ATP) channels can protect the brain or cultured neurons against a variety of anoxic or metabolic challenges. However, little is known about the subunit composition or functional regulation of the channel itself. In the present study, we sought to characterize the mitoK(ATP) channel in the mouse brain using overlapping approaches. First, we determined that mitochondria contain the pore-forming Kir6.1 and Kir6.2 subunits with Western blotting, immunogold electron microscopy and the identification of mitochondrial transport sequences. In contrast, we found no evidence for the presence of either known sulfonylurea receptors (SUR1 or SUR2) in the mitochondria. However, the ATP-dependent K (K(ATP)) channel inhibitor glibenclamide specifically binds to mitochondria in both neurons and astrocytes, and small molecular weight SUR2-like proteins were concentrated in mitochondria. In addition to mice, similar results were found in rats and pigs. Second, live respiring mitochondria were stained with the membrane potential sensitive dye MitoFluorRed and visualized by confocal microscopy. We investigated the effects of pharmacological closing and opening of the channel with glibenclamide and the specific mitoK(ATP) openers diazoxide and BMS-191095. Closing of the channel inhibited the energization of the mitochondria, which was reversed by the application of the mitoK(ATP) openers. We also found that blocking mitochondrial peroxynitrite formation with FP15 has a similar effect to blocking the mitoK(ATP) channels. We conclude that brain mitochondria contain functional K(ATP) channels. The pore-forming subunit of the channel can be either Kir6.1 or Kir6.2, and the SUR subunit may be a SUR2 splice variant or a similar protein.