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Apoptosis is a programmed cell death which has a critical role in embryonic development and maintenance of homeostasis in various cells and tissues. The mitochondrian is the cellular power plant providing ATP for most processes requiring energy and also, has a decisive role in the regulation of apoptosis by controlling the release of some mitochondrial proteins such as cytochrome c, AIF, Smac/ Diablo, and Omi/HtrA2. Studies in mice gene-deleted for Omi/HtrA2 and AIF showed the involvement of these mitochondrial proteins in selective cell degeneration in the striatum and celebellar neurons. Mutation in the mitochodrial AAA protease gene, paraplegin, caused an autosomal form of hereditary spastic paraplegia and a distinctive apoptosis in corticospinal neuronal axon. Reactive oxygen species and a fault of respiratory chain in mitochondria contribute to various neurological disorders. However, the pathogenetic mechanisms of selective neurodegeneration is not completely known. The elucidation of biological functions of mitochondrial proteins may shed new light on the development of novel drug for the prevention and therapy for the human neurological diseases. (Cancer Prev Res 11, 256- 263, 2006)