Early in mitochondria-mediated apoptosis, the mitochondrial outer membrane becomes permeable to proteins that, when released into the cytosol, initiate the execution phase of apoptosis. Proteins in the Bcl-2 family regulate this permeabilization, but the molecular composition of the mitochondrial outer membrane pore is under debate. We reported previously that at physiologically relevant levels, ceramides form stable channels in mitochondrial outer membranes capable of passing the largest proteins known to exit mitochondria during apoptosis (Siskind, L. J., Kolesnick, R. N., and Colombini, M. (2006) Mitochondrion 6, 118 -125). Here we show that Bcl-2 proteins are not required for ceramide to form protein-permeable channels in mitochondrial outer membranes. However, both recombinant human Bcl-x L and CED-9, the Caenorhabditis elegans Bcl-2 homologue, disassemble ceramide channels in the mitochondrial outer membranes of isolated mitochondria from rat liver and yeast. Importantly, Bcl-x L and CED-9 disassemble ceramide channels in the defined system of solvent-free planar phospholipid membranes. Thus, ceramide channel disassembly likely results from direct interaction with these anti-apoptotic proteins. Mutants of Bcl-x L act on ceramide channels as expected from their ability to be anti-apoptotic. Thus, ceramide channels may be one mechanism for releasing pro-apoptotic proteins from mitochondria during the induction phase of apoptosis.Apoptosis is required for normal development and tissue homeostasis in multicellular organisms. Deregulation of apoptosis is fundamental to many diseases, such as cancer, stroke, heart disease, neurodegenerative disorders, autoimmune disorders, and viral diseases. During apoptosis, DNA fragments and other contents of the cell are packaged into apoptotic bodies that are consumed by phagocytosis. There are two main pathways for apoptosis, namely the extrinsic receptor-mediated pathway and an intrinsic mitochondria-mediated one. There is also cross-talk between these two pathways. The intrinsic pathway is initiated when one or more of a multitude of signals converge on mitochondria that ultimately result in an increase in the permeability of the mitochondrial outer membrane (MOM).2 This permeabilization leads to the release of intermembrane space proteins, including cytochrome c, procaspases, apoptosis-inducing factor, heat shock proteins, Smac/ Diablo, and endonuclease G (1). In the cytosol, these proteins activate caspases and DNases that carry out the execution phase of apoptosis.The mechanism for the increased permeability of the MOM during the induction phase of apoptosis is currently highly debated. Several mechanisms have been proposed to explain how mitochondrial intermembrane space proteins are released into the cytosol to facilitate apoptotic cell death. Some involve direct pore formation in the MOM. Several candidate pores exist, but most involve activated multidomain pro-apoptotic Bcl-2 family proteins, Bax and Bak (for example see Refs. 2-5). Another model for MOM permeabil...