In the present study, a cDNA microarray technology was used to analyze the gene expression profile in ischemia and in electroacupuncture (EA)-treated ischemia. A focal cerebral ischemia/reperfusion model on Macaca mulatta was performed with a modified middle cerebral artery occlusion method. Among the nearly 8000 genes, approximately 8% of the total number of genes examined were affected after ischemia/reperfusion injury. Major altered genes were downregulated. In EA-treated monkeys, approximately 10% of the total number of genes examined were affected. Major altered genes were upregulated, including signal transduction-, cell-cycle-, metabolism-, stress response-, DNA repair-related genes. One of the representative upregulated genes encodes insulin-like growth factor-1 (IGF-1) was confirmed using in situ hybridization. Results showed that after ischemia/reperfusion injury, IGF-1 mRNA expression decreased in ipsilateral striatum, whereas increased in ipsilateral hippocampus. No expression changes were observed in cortex. EA treatment could obviously upregulate the IGF-1 mRNA expression in striatum, and further enhance its expression in hippocampus. Therefore, the data presented suggest a possible mediator underlying the mechanisms of anti-ischemic effect of acupuncture. In conclusion, the protective mechanisms of EA against stroke include several related pathways and gene expressions. Microarray analysis may provide a framework for understanding these complicated mechanisms and yield valuable, clinically relevant insights and potentially therapeutic targets of stroke.