Mitochondrial permeability transition (PT) is a central event in apoptosis. This study shows that PT, which involves the opening of PT pores and the disruption of the mitochondrial transmembrane potential (ΔΨm), is critical for the apoptotic cascade. The inhibitor bongkrekic acid (BA), which blocks PT, prevents various apoptotic phenomena, including ΔΨm disruption, glutathione depletion, reactive oxygen species (ROS) generation, NFκB translocation, phosphatidylserine exposure, cytoplasmic vacuolization, chromatin condensation, and DNA fragmentation. These findings suggest that many apoptotic events are secondary to PT. Additionally, the study indicates that ΔΨm disruption is secondary to transcriptional events, linking PT to the p53 and ICE/Ced3 control points of apoptosis. PT is positioned upstream of nuclear and plasma membrane features of programmed cell death (PCD). The study also shows that proteases from the ICE/Ced3 family act upstream of mitochondria, as their inhibition prevents ΔΨm dissipation. BA, which mimics the effects of Bcl-2, inhibits apoptosis in thymocytes, both in vitro and in vivo. The results highlight PT as a critical checkpoint in the apoptotic cascade, with implications for understanding the regulation of apoptosis.Mitochondrial permeability transition (PT) is a central event in apoptosis. This study shows that PT, which involves the opening of PT pores and the disruption of the mitochondrial transmembrane potential (ΔΨm), is critical for the apoptotic cascade. The inhibitor bongkrekic acid (BA), which blocks PT, prevents various apoptotic phenomena, including ΔΨm disruption, glutathione depletion, reactive oxygen species (ROS) generation, NFκB translocation, phosphatidylserine exposure, cytoplasmic vacuolization, chromatin condensation, and DNA fragmentation. These findings suggest that many apoptotic events are secondary to PT. Additionally, the study indicates that ΔΨm disruption is secondary to transcriptional events, linking PT to the p53 and ICE/Ced3 control points of apoptosis. PT is positioned upstream of nuclear and plasma membrane features of programmed cell death (PCD). The study also shows that proteases from the ICE/Ced3 family act upstream of mitochondria, as their inhibition prevents ΔΨm dissipation. BA, which mimics the effects of Bcl-2, inhibits apoptosis in thymocytes, both in vitro and in vivo. The results highlight PT as a critical checkpoint in the apoptotic cascade, with implications for understanding the regulation of apoptosis.