Expression of the estrogen receptor (ER) in the preoptic area (POA) and the mediobasal hypothalamus (MBH) in newborn female rats was studied by immunohistochemistry (IHC) and in situ hybridization histochemistry (ISHH). The number of ER immunoreactive (ER-IR) cells decreased and expression of ER mRNA was suppressed in the arcuate (ARH) and the ventromedial (VMH) hypothalamic nuclei by daily injections of estradiol benzoate (EB) for ten consecutive days. In contrast, in the POA, expression of ER mRNA was not suppressed by EB treatment, while the ER immunoreactivity and the number of ER-IR cells were decreased by the treatment. Results of quantification of ER mRNA by reverse transcription-polymerase chain reaction correlated well with results from ISHH, that is, ER mRNA expression decreased in the MBH but not in the POA. Thus, estrogen affects ER gene expression in different ways in these two brain regions.