rTMS is a noninvasive technique to induce electric current in the brain and is supposed to be beneficial for the treatment of patients with depression, schizophrenia and neurodegenerative disorders. We reported previously that rTMS modulates monoamine tranporter. However, the mechanisms underlying the effects of rTMS are still unclear. We analyzed the changes in mRNA expression in mouse brain that occurred after rTMS with an Affymetrix GeneChip. Following 20days of rTMS, many genes were differentially expressed in the mouse brain. Down-regulation of Period 2, 3 and hypocretin mRNA expression levels and a subsequent decrease in food and water intake were observed. HSP70 mRNA expression levels were up-regulated after transient and chronic rTMS. In N2A 150Q cells, an up-regulation of HSP70 mRNA and protein levels and subsequent cell-protective effects were observed after chronic rTMS. In addition, dopamine receptor 2 mRNA expression levels were down-regulated, and a subsequent decrease in the binding of [3H]raclopride was observed. A decrease in the Bmax and no change in the KD of [3H]raclopride binding was observed in the binding assay. These results indicated that the modulation of several genes may be involved in the therapeutic mechanisms of acute and chronic rTMS for patients with neuropsychiatric disorders.