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It has been hypothesized that decreased neurogenesis in the dentate gyrus may be involved in mediating depressive disorders, which are 1.5-3 times more frequent in women than in men. Additionally, prenatal stress may increase the risk of developing depression in adulthood. However, the interrelations between prenatal stress and the development of depression in adulthood, preferentially in females, are not understood. Here, we subjected pregnant rats to a single 20-min period of restraint stress on day 18 after mating. When the offspring were 75 days of age, the numbers of granule cells and pyramidal cells (area CA1-3) in the hippocampus were analyzed with the optical fractionator. The Cavalieri's principle was applied to analyze the volumes of both granule cell layer and pyramidal cell layer in the hippocampus. Prenatally stressed females, but not males, had reduced numbers of hippocampal granule cells compared to their non-prenatally stressed counterparts. This is the first report of a sex-specific difference concerning the reduction of the number of hippocampal granule cells due to prenatal stress. In humans, prenatal stress may induce cell loss in the granule cells of the hippocampus preferentially in females compared to males, and this may be a sex-specific predisposing factor for the development of depression in adulthood.