Mitochondria play a central role in apoptotic signaling pathways. Upon exposure to apoptotic stimuli, mitochondria release cytochrome c to the cytoplasm and activate caspase cascade leading to cell death. However, the events upstream of cytochrome c release are not fully understood. Here, we quantitate mitochondrial aggregation in situ using a novel laser scanning cytometry technique and reveal that mitochondria aggregate during apoptosis in a budding-like shape. The quantitative analysis reveals that mitochondrial aggregation is not inhibited by caspase-3 inhibitor ZEVD. Furthermore, bcl-x(L) transfection cannot suppress mitochondrial aggregation. However, overexpression of bcl-x(L) inhibits cytochrome c release from mitochondria. Therefore, mitochondrial aggregation is an event upstream of cytochrome c release during apoptosis. This mitochondrial aggregation was not observed in human leukemia H9 cells where apoptosis occurs in a mitochondria-independent fashion. Our studies imply that changes in the localization of mitochondria participate in the regulation of apoptosis through cytochrome c release.