Much attention has been focused on the mitochondrial superoxide anion (O2-), which is also a critical free radial produced by ionizing radiation. The specific role of the mitochondrial O2- on physiological aging in mammals is still unclear despite wide-spread evidence that oxidative stress is involved in aging and age-related diseases. The major endogenous source of O2- is generated as a byproduct of energy metabolism from mitochondria. In order to better understand how O2-relates to metazoan aging, we have comprehensively examined age-related changes in the levels of oxidative damage, mitochondrial O2- production, mitochondrial antioxidant enzyme activity and apoptosis induction in key organs of an inbred mouse strain (C57BL/6J). Oxidative damage accumulated and excess apoptosis occurred in the brain, oculus and kidney with aging, but comparatively little occurred in the heart and muscle. These rates are correlated with O2- levels. Mitochondrial O2- production levels increased with aging in the brain, oculus and kidney, and did not significantly increased in the heart and muscle. In contrast to O2- production, mitochondrial SOD activities increased in heart and muscle, and remained unchanged in the brain, oculus and kidney with aging. These results suggest that O2- production has high organ specificity, and oxidative damage by O2- from mitochondria mediated apoptosis can lead to organ atrophy and physiological dysfunction. In addition, O2- from mitochondria plays a core role in physiological aging.