The major biochemical process of apoptosis involves the activation of a group of proteases (caspases) and the selective cleavage of a set of intracellular proteins that leads to the collapse of cell survival mechanism. Among the caspases identified, caspase-3 stands out because it is commonly activated by numerous death signals and cleaves a growing number of cellular components. In order to reveal potential targets of caspase-3 in primate neural tissue, an alternative cell free system based on adult monkey brain was established to reproduce the downstream part of apoptotic program, initiated by the addition of granzyme B. Through Western blot analysis, caspase-3 was found to become mature in a two-step manner and its activity was exhibited by the cleavage of the synthetic substrate, Ac-DEVD-pNA. Investigations on native proteins in the brain extract showed that poly (ADP-ribose) polymerase (PARP) was cleaved to an 85 ku fragment, suggestive of caspase-3 activity. And more intriguingly, a neuronal apoptosis inhibitory protein (NAIP)-immunoreactive fragment with molecular mass of approximately 40 ku was detected in granzyme B-treated brain extract and its production was not blocked by the caspase-3 inhibitor, Ac-DEVD-CHO. According to the substrate specificity of granzyme B and the size of cleavage product, putative cleavage site may be located immediately after the third DIR domain of NAIP. These data suggest that cleavage events involved in apoptosis can be reproduced in matured primate brain extract and NAIP is likely to be the target of granzyme B, but not of caspase-3, during apoptosis.