Estrogen is important for numerous physiological actions, most of which are mediated via the nuclear estrogen receptors (ERs), ER-alpha and ER-beta, which modulate the transcription of target genes following estrogen binding. Estrogen functions change with age. In the present study, to reveal the effects of normal aging on ER-beta expression in the brain, we examined ER-beta expression at the transcriptional level using young (10 weeks), middle-aged (12 months) and old (24 months) intact female rats. In situ hybridization using a digoxigenin-labeled RNA probe was used to assess the number of ER-beta mRNA-positive cells in each region in whole brain. ER-beta mRNA-positive cells were detected throughout the brain in young female rats and were reduced in number in the olfactory bulb, cerebral cortex, hippocampus, accumbens nucleus, part of the amygdala and raphe nucleus of middle-aged rats but did not decline further in number in aged animals. By contrast, the number of ER-beta mRNA-positive cells in the hippocampus, caudate putamen, claustrum, accumbens nucleus, substantia nigra and cerebellum was not significantly different between young and middle-aged rats but was decreased in old rats. These results indicate that the expression of ER-beta mRNA in the female rat brain is differentially modulated during aging and that the changes are region specific.