We studied the mechanism of intra-mitochondrial death initiator caspase-9 activation by a redox response, in which hydrogen peroxide (H(2)O(2)) caused a subtle decrease in the inner membrane potential (Deltapsim) with little evidence of cytochrome c release. Initiation of the intra-mitochondrial autocleavage of procaspase-9 preceded the onset of caspase cascade induction in the cytosol. Purified mitochondria demonstrated procaspase-9 processing and releasing abilities when exposed to H(2)O(2). Bcl-2 overexpression caused accumulation of the active form caspase-9 in the mitochondria, rendering the cells resistant to the redox stress. Intriguingly, disulfide-bonded dimers of autoprocessed caspase-9 were generated in the mitochondria in the pre-apoptotic phase. Using a substrate-analog inhibitor, dimer formation of procaspase-9 was also detectable inside the mitochondria. Furthermore, thiol reductant thioredoxin blocked the caspase-9 activation step and the cell death induction. Thus, redox stress-responsive thiol-disulfide converting reactions in the mitochondrion seemed to mediate procaspase-9 assembly that allows autoprocessing. This study offers an explanation for the recent observation that Apaf-1-null cells can execute apoptosis, which can be blocked by Bcl-2, and supports the proposition that the cytochrome c-Apaf-1-procaspase-9 complex functions in the caspase amplification rather than in its initiation.