Abstract: With the development of molecular biology, genome science becomes an important subject currently. Characterized by high-throughput, high-integration, high-parallelism, miniaturization and automation, it is the integrated study of gene properties on a large scale. Stroke, an important cerebral vascular disease, is one of the threats to human health. The utilization of microarray study for the pathogenesis of stroke, not only reveals the essentials of the disease in the overall level of genes, but also contributes to the detection of therapeutic targets and the development of novel drugs for stroke. Referring to our own work, this discussion focuses on the progress of the mechanisms underlying experimental cerebral ischemia investigation in vivo as well as anti-cerebral ischemia agents by gene chip technology.