Although DNA microarray studies showed up-regulation of various genes, failures of translation of many genes are expected to occur under ischemic conditions even in the penumbra with mild reduction in cerebral blood flow. We applied surface enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF-MS) technology to study proteomic profile at 6, 12, and 24 h after photothrombotic middle cerebral artery (MCA) occlusion with or without YAG laser-induced reperfusion in adult male spontaneously hypertensive rats. Of the 43 protein peaks that differed from the sham-operation group with a criterion (no overlap of peak intensities between the two groups), 36 peaks (84%) were down-regulated, and seven were up-regulated. All increased peaks showed greater than twofold increases (up to 8.1 fold) compared with those in the sham-operation group. Effects of reperfusion were observed mainly at 24 h after 1 h of MCA occlusion only in the penumbra, where 23 of 32 peaks returned toward the control values, whereas none of 33 peaks showed such attenuation in the ischemic core. Major ischemia-induced changes in protein peaks detected with SELDI-TOF-MS were down-regulations. The present study showed that dynamic changes of protein profile were associated with progression and recovery of the ischemic core and penumbra.