An antibody microarray was used to analyze potential modifications in brain protein levels induced by ischemic reperfusion. Total brain extracts from rats subjected to 15 min of transient global ischemia followed by 3 days of reperfusion and sham control animals were compared within the same array. Separate arrays were run to analyze resistant (cortex) and vulnerable (CA1) regions to ischemia. Candidate components distinguishing the two cellular populations were selected under stringent criteria. IR significantly decreased the expression of Bcl-x, caspase 11, GADD153, Cdk4, E2F1, Retinoblastoma-P, SMAD4, AP-1/c-jun, ATF2, PCAF, MAP1b and cofilin within both regions. NGF and NMDA 2A receptors and IkappaB were specifically down-regulated in CA1, while Pyk2-P, b-NOS, and tyrosine hydroxylase were slightly up-regulated in the same region. Some of the array results were validated by western blot. Both the array and western blot results suggested a relevant IR induced activation of calpain specifically at CA1.