Subcortical regions such as the medial septum-diagonal band of Broca and supramammillary area have been shown to mediate indirect oestrogenic effects on hippocampal morphology and function. Here, the role of the median raphe (MR), a serotonergic subcortical structure, is studied. To this end, 17beta-estradiol-filled 30-gauge cannulae were implanted into the MR of female ovariectomized rats; cholesterol-filled cannulae served as controls. After seven days, using unbiased electron microscopic stereological calculations and semiquantitative analysis, the spine synapse density and surface density of glial fibrillary acidic protein-positive astrocyte processes, respectively, were determined in the stratum radiatum of the CA1 region of the hippocampus. Changes in the serotonergic innervation of the hippocampal CA1 region were determined by immunohistochemistry and subsequent morphometric analysis. In the stratum radiatum of the CA1 region, local estradiol application into the MR resulted in a 47% increase in spine synapse density. Simultaneously, the density of glial fibrillary acidic protein-positive fibers decreased by 16%. The density of serotonin (5-HT) innervation of the strata lacunosum moleculare and radiatum of the CA1 region of the hippocampus was reduced in response to estradiol, as shown by a decrease in the length of fibers (27.6 and 48.3% decrease, respectively) and the number of large varicosities (32.5 and 38.8% decrease, respectively). These observations suggest a major role of the MR in mediating oestrogenic effects on the hippocampus and an involvement of the serotonergic system.