An intraperitoneal (ip) injection of kainic acid (45 mg/kg), which generates reactive oxygen species in brain produced broad-spectrum limbic and severe sustained seizures and mitochondrial DNA (mtDNA) damage in all of the treated mice. These seizures and mtDNA damage were completely abolished by an intracerebroventricular (icv) injection of ganglioside GT1b [4], a potent inhibitor for glutamate receptor-mediated activation and translocation of protein kinase or lipid peroxidation, by an ip injection of melatonin [4], a potent scavenger of hydroxyl radicals (·OH) and by an ip injection of a substrate (1g/kg) of enzymes on the Krebs cycle including α-ketoglutarate, oxaloacetate, succinate, malate, fumarate and citrate. However, preinjection of maleate (1g/kg) or malonate (1g/kg), which is non-component on the Krebs cycle did not prevent against kainic acid-induced seizures. Furthermore, although in vivo and in vitro exposure of mouse brain to kainic acid elicited an increase in lipid peroxidation, the increased lipid peroxidation was completely inhibited by the co-treatement with melatonin, ganglioside GT1b, α-ketoglutarate, oxaloacetate, succinate, malate, fumarate or citrate but not maleate or malonate. 2-methylcitrate (2-MC:1.0, 5.0 or 10.0mM), an inhibitor of enzymes such as citrate synthase, aconitase and isocitrate dehydrogenase on the Krebs cycle, inflicted damage to mtDNA in the brain frontal cortex in a concentration dependent manner. The brain mtDNA damage induced by 2-MC was not prevented by citrate. Icv injection of 2-MC (9 µmol/animal) also caused damage to brain mtDNA, increased lipid peroxidation and seizures in mice. 2-MC-induced seizures, brain mtDNA damage and lipid peroxidation were not prevented by ip pre-injection of citrate (1g/kg). These results suggest that the Krebs cycle may play a key role for protection against seizures and subsequent brain mtDNA damage induced by the excitotoxic/neurotoxic agent, kainic acid, a potent producer of reactive oxygen species including ·OH.