Chronic ethanol treatment caused a differential modulation of apoptosis-associated proteins, cytochrome c release, concomitant with procaspase-9 and procaspase-3 activation leading to oligonucleosomal DNA fragmentation in rat cerebral cortex and cerebellum. Caspase-3 proform (32 kDa) showed decreased immunoreactivity in cortex and cerebellum, while the cleaved active fragment (17 kDa) increased significantly in cerebellum after ethanol treatment. Further, chronic ethanol treatment increased caspase-3 activity in cortex and to a higher extent in cerebellum, which was further confirmed by blocking experiments with caspase-3 specific inhibitor, N-acetyl-Asp-Glu-Val-Asp-aldehyde (Ac-DEVD-CHO). We tested whether activated caspase-3 cleaves downstream substrates such as poly (ADP-ribose) polymerase-1 and protein kinase C-delta (PKC-delta). Western blots showed poly (ADP-ribose) polymerase-1 cleavage to its signature fragment of 85 kDa and decreased levels of PKC-delta in cerebral cortex and cerebellum after ethanol treatment, suggestive of caspase-3 activation. Elevated caspase-3 activity in cerebellum than cortex correlating with cytochrome c, caspase-9, active caspase-3 (p17), poly (ADP-ribose) polymerase-1 and PKC-delta data, suggests a mechanism by which ethanol might be exerting pro-apoptotic events in brain and how selective brain regions such as cerebellum are vulnerable to ethanol neurotoxicity in terms of cell death.