Although the estrogen receptor (ER) is a major target for actions of estrogen on the brain, little is known about its neural expression during aging, when levels and the mode of estrogen release undergo substantial changes. Therefore, in the present study, we examined effects of aging and estrogen treatment on the numbers of cells expressing the ER in female rats. Two regions relevant to reproductive function were analyzed: the anteroventral periventricular nucleus (AVPV), and the principal nucleus of the bed nucleus of the stria terminalis (pBST). Numbers of ER-expressing cells were quantified using an unbiased stereological approach. Female rats were used at three ages (young (3-4 mo), middle-aged (10-12 mo) or old (24-26 mo)), with or without estrogen replacement. Because the estrogen milieu impacts the function of neurotransmitter receptors such as the NMDA receptor (NMDAR) in the brain, we also investigated the co-localization of ER and the obligatory NMDAR subunit, NR1. We observed a significant age-related decrease in ER cell number in the AVPV but not the pBST. No significant effect of estrogen on ER cell number was detected in either brain region at any age. Approximately 10% and 3% of cells expressing ER also co-expressed NR1 in AVPV and pBST, respectively, and this did not differ with age or treatment. Taken together, our results demonstrate: 1) age-related changes in ER cell number that are region-specific; 2) this expression is not altered by estrogen replacement; and 3) a subset of ER positive cells co-express NR1.