Abstract.Estrogen plays an important role in sexual differentiation of the brain in rats during the perinatal period. To elucidate molecular mechanisms underlying sexual differentiation of the brain, in this study we investigated genes differentially expressed between sexes or induced to express by estrogen in neonatal rat hypothalamus using DNA microarray analysis in combination with real-time RT-PCR. It was found that the levels of expression of the genes encoding glutamic acid decarboxylase 65 and coronin 1b were higher in male than female hypothalamus on postnatal day (PN) 5 and those of collagen type 3 α1 and thioredoxin reductase 2 genes in female hypothalamus on PN5 were decreased and increased, respectively, by treatment with estradiol on PN2. Then the developmental changes in the expression of these 4 genes were examined from 1 day before the parturition to PN9, and they all showed sexual dimorphic patterns. In addition, dependence of the expression of these genes on either estradiol, testosterone or dihydrotestosterone during the neonatal period was confirmed. These results suggest that these four genes are involved in sexual differentiation of the rat brain, and that androgen per se as well as estrogen may take part in the processes. Key words: DNA microarray, Gene expression, Estrogen, Androgen, Sexual differentiation of brain (J. Reprod. Dev. 49: [547][548][549][550][551][552] 2003) exual differentiation of rat brain occurs during the perinatal period, i.e., around the day of birth to one week after birth, which is known as the critical period. In the male rat, testosterone secreted from the testis during the critical period induces the masculinization of the brain, while in the female, the absence of testosterone results in feminization of the brain [1,2]. It has been demonstrated that aromatization of testosterone to estradiol in the brain plays an important role in mediating the effects of testosterone [3]. It is well known that estradiol affects many aspects of neuronal differentiation including apoptotic cell death [4], cell migration [5], synapse formation [6], and neurogenesis [7]. Most of these effects of estradiol occur through interactions with estrogen receptors, which serve as transcription factors for a wide variety of target genes [8]. To elucidate the molecular mechanism of sexual differentiation of the brain, it is important to study signaling cascades regulated by estradiol during the critical period. In this context, we have previously identified the granulin precursor gene as an estradiol-as well as testosterone-inducible gene in the rat hypothalamus during the critical period [9][10][11].T e s t o s te r o n e c a n b e c o n v e r t e d t o 5α -dihydrotestosterone (DHT), a non-aromatizable androgen, by 5α-reductase in the neonatal brain [12], but the significance of androgen or androgen receptors in the sexual differentiation of the brain is