Previous studies have demonstrated that ischemic stroke increases beta-amyloid (Abeta) production by increasing beta-secretase (BACE1) through activation of caspase-3, and stimulates generation of mutant ubiquitin (UBB(+1)) in rat brains. In this study, we examined whether caspase-3 activation participates in the regulation of UBB(+1) generation and UBB(+1)-mediated BACE1 stability in ischemic injured brains. The results showed that UBB(+1) and activated caspase-3-immunopositive-stained cells were time dependently increased in the ipsilateral striatum of rat brains after middle cerebral artery occlusion. UBB(+1)-immunopositive cells could be co-stained with caspase-3, Abeta (UBB(+1)-Abeta), and BACE1 (UBB(+1)-BACE1). BACE1 protein could also be pulled down by immunoprecipitation with UBB(+1) antibody. Z-DEVD-FMK (DEVD), a caspase-3 inhibitor, significantly decreased the level of UBB(+1) protein and the number of UBB(+1)-Abeta and UBB(+1)-BACE1 double-stained cells in the ischemic striatum, as well as the level of UBB(+1)/BACE1 protein complex. We conclude that activation of caspase-3 might be upstream of UBB(+1) formation and that excessive UBB(+1) could bind to BACE1 and increase the stability of BACE1, thereby increasing Abeta in ischemic injured brains. These results suggest new biological and pathological effects of caspases and regulation of the ubiquitin-proteasome system in the brain. Our results provide new therapeutic targets to prevent further neurodegeneration in patients after stroke.