The present study was conducted to investigate the mRNA expression of the two estrogen receptor (ER) subtypes ERalpha and ERbeta in the brain of Japanese quail embryos. We found expression of both ERalpha and ERbeta mRNA in homogenate of whole head from 6-day-old embryos, and in brain homogenate from 9- and 12-day-old embryos using real-time PCR. In 9- and 12-day-old embryos the ERalpha expression was higher in females than in males. We used in situ hybridization to examine the localization of the ERs in sections from male and female brains on day 9 and day 17 of incubation. On day 9, ERbeta mRNA was detected in the developing medial preoptic nucleus (POM), in the medial part of the bed nucleus of the striae terminalis (BSTm), and in the tuberal region of the hypothalamus. ERalpha signal could not be detected in the POM, the BSTm or the tuberal region in 9-day-old embryos. In 17-day-old embryos, ERbeta was highly expressed in the preoptic area, the nucleus Taeniae of the Amygdala (TnA) and the BSTm. Expression of ERalpha mRNA was detected in parts of the preoptic area and in the telencephalic TnA. No ERalpha expression was found in the BSTm, an area known to be sexually dimorphic in adults. The high embryonic expression of ERbeta in brain areas linked to sexual behavior indicates that ERbeta plays a role in sexual differentiation of the Japanese quail brain.