It is well established that estrogen affects hippocampal long-term potentiation and hippocampus-related memory processes. Furthermore, theta rhythm, in conjunction with long-term potentiation, influences memory and is regulated by subcortical structures, including the median raphe and supramammillary area. To test the validity of the hypothesis that the effects of estrogen on the hippocampus are mediated, at least partly, via these subcortical structures, it must first be determined whether the neurons of the median raphe and supramammillary area contain estrogen receptors. Light and electron microscopic double immunostaining for estrogen receptor-alpha plus serotonin and estrogen receptor-alpha plus calretinin on vibratome sections of the median raphe and supramammillary area, respectively, demonstrated that large populations of the median raphe serotonin and supramammillary area calretinin neurons exhibit estrogen receptor-immunoreactive nuclei. These observations indicate that circulating gonadal hormones can affect hippocampal electric activity indirectly, via those subcortical structures that are involved in theta rhythm regulation.