Apoptosis is critical for normal development and tissue homeostasis. However, its abnormal occurrence has been implicated in a number of disorders, including neurodegenerative diseases and stroke. Translocation of cytochrome c (Cyt c) from mitochondria to the cytoplasm is a key step in the initiation and/or amplification of apoptosis. Here we discuss Cyt c release in apoptosis with its impact on the CNS and review our studies of Cyt c release from isolated rat brain mitochondria in response to several insults. Calcium-induced Cyt c release, as occurs in neurons during stroke and ischemia, involves rupture of the mitochondrial outer membrane (MOM) and can be blocked by inhibitors of the mitochondrial permeability transition (mPT). Thus, inhibitors of the mPT have shown efficacy in animal models of ischemia. In contrast, proapoptotic proteins, such as BID, BAX, and BAK, induce Cyt c release independently of the mPT without lysing the MOM. Several inhibitors of BAX-induced Cyt c release have shown promise in models of CNS apoptosis. Because of their distinct mechanisms for Cyt c release, both the mPT and proapoptotic proteins should be targeted for effective clinical intervention in CNS disorders involving apoptosis.