Many environmental and therapeutic agents initiate apoptotic cell death by inducing the release of cytochrome c from the mitochondria, which activates Apaf-1 (apoptotic protease-activating factor-1). This large (approximately 130kD) protein is a mammalian homologue of CED-4, an essential protein involved in programmed cell death in the nematode C. elegans. Cytochrome c activates Apaf-1, which oligomerizes to form an approximately 700-1400-kDa caspase-activating complex known as the Apaf-1 apoptosome. Caspase-9, an initiator caspase, is then recruited to the complex by binding to Apaf-1 through CARD-CARD (caspase recruitment domain) interactions to form a holoenzyme complex. Subsequently, the Apaf-1/caspase-9 holoenzyme complex recruits the effector caspase-3 via an interaction between the active site cysteine in caspase-9 and the critical aspartate, which is the cleavage site for generating the large and small subunits of caspase-3 that constitute the activated form of caspase-3. This initiates the caspase cascade that is responsible for the execution phase of apoptosis. Intracellular levels of K+, XIAP an inhibitor of apoptosis protein, and at least two mitochondrial released proteins, Smac/DIABLO and Omi/Htra 2 a serine protease, tightly regulate formation and function of the apoptosome. Thus, a number of physiological mechanisms ensure that the apoptosome complex is only fully assembled and functional when the cell is irrevocably committed to die. It is interesting that more recent studies show that a variety of small molecules can directly activate or inhibit caspase activation by interfering with the formation and function of the apoptosome complex. The cytotoxicity of many conventional chemotherapeutic drugs rests on their ability to induce apoptosome formation and apoptosis. Defects in this pathway can result in drug resistance, and the discovery that small molecules can directly activate or inhibit the apoptosome may provide new alternative treatments for cancer.