Estrogen has an important effect on higher brain function such as memory, learning, and emotion in which the hippocampus plays a critical role. The hippocampus expresses estrogen receptors, ER α and ERβ, which are ligand-dependent transcription factors; however, the precise mechanism of estrogen action is not fully understood. We explored genes which are up-regulated by estrogen in the hippocampus using ovariectomized rat models. Microarray analysis revealed that mRNA levels of ectonucleotide pyrophosphatase/phosphodiesterase 2 (Enpp2), insulin like growth factor 2 (Igf2) and insulin-like growth factor binding protein 2 (Igfbp2) were increased by estrogen in the hippocampus. Quantitative-PCR analysis demonstrated that the levels of Enpp2, Igf2 and Igfbp2 mRNA were elevated by estrogen administration in the hippocampus but not in the hypothalamus. On the other hand, ERα, ERβ and progesterone receptor (PR) mRNA expression was up-regulated by estrogen only in the hypothalamus. We further analyzed the time-dependent regulation of these genes using rat pituitary adenoma, MtT/S and GH3 cells, which are known to express ERα. In both MtT/S and GH3 cells, Igfbp2 and Enpp2 mRNAs were up- and down-regulated by estrogen, respectively, whereas Igf2 mRNA was increased only in GH3 cells. These results demonstrate a brain region- and cell type-specific responses to estrogen in rat brain, suggesting that Igf signaling may mediate the estrogen function in the hippocampus.