Abnormal levels of brain-derived neurotrophic factor (BDNF) are associated with major depression, a disorder with a higher incidence in women than men. Stress affects BDNF levels in various brain regions and thus, a heightened stress response in females could contribute to the development of depression. As well, ovarian hormones directly affect brain levels of BDNF mRNA and protein. Two experiments were performed to investigate the effects of stress and sex and gonadal hormones on BDNF protein levels in CA1, CA3, and dentate gyrus (DG) subregions of the hippocampus. In the first experiment, male and female Sprague-Dawley rats were subjected to one hour of restraint stress or control handling prior to sacrifice. In the second experiment, fifty-one female rats were ovariectomized and separated into stress and control conditions, as described for the first experiment. Stressed and handled groups received a single injection of estrogen (E; 53h prior to stress), estrogen and progesterone (EP; E given at 53h and P given 5h prior to stress), or vehicle (OVX). In both experiments BDNF protein was quantified using an enzyme-linked immunosorbent enzyme assay (ELISA) in micropunches of hippocampus. Gonadally intact females had significantly higher levels of BDNF in CA3, but significantly lower levels in DG, relative to males. In CA3, stress significantly decreased BDNF in both males and females. In DG of ovariectomized female rats, the effects of stress were significantly different following EP vs. vehicle treatment. Thus, stress increased BDNF levels in EP-treated rats but decreased BDNF levels in vehicle-treated rats. Reduced trophic support in DG in the presence of estrogen and progesterone could jeopardize neurogenesis and under certain conditions could be a contributing factor to the hippocampal atrophy associated with stress-induced affective disorders. These results emphasize the need to consider sex, gonadal steroids, and hippocampal subregion when examining the effects of stress on the brain.