Ischemic stress in the brain causes acute and massive cell death in the targeted core area followed by a second phase of damage in the neighboring penumbra. The purpose of this study was to examine the global gene expression patterns in the penumbra, because the ischemic lesion in this region could be rescued by restoration of blood flow and other protective therapies. Adult C57Bl/6 mice were subjected to a 90-min middle cerebral artery occlusion (MCAO). Laser capture microdissection (LCM) was used for tissue dissection at 4 and 24 hr after reperfusion. Sham-operated animals were used as controls. Gene expression in the penumbra was examined by using microarray analysis and quantitative RT-PCR. In agreement with previous reports, most genes were down-regulated at 4 hr after the onset of reperfusion in the ischemic penumbra compared with controls. In contrast, at 24 hr after reperfusion, most genes were up-regulated in the ischemic penumbra. Several genes not previously reported to be associated with ischemia were found. The gene lists generated in this study will help us to understand better the spatial and temporal distribution of molecules involved in the ischemic cascade. Published 2008 Wiley-Liss, Inc.