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Sex plays a major role in stress integration and stress-related affective disease states. Notably, neurocircuits regulating organismic responses to stress are prime targets for central gonadal steroid action. To assess the roles of sex and estrous cycle in central stress integration, we analyzed c-fos mRNA expression in hypothalamic-pituitary-adrenocortical-related regions of stressed male and cycling female (proestrous, estrous, and diestrous) rats. At 60 min after the onset of acute restraint stress, all animal groups showed induction of c-fos mRNA in the frontal cortex, cingulate cortex, piriform cortex, hippocampus, hypothalamic paraventricular nucleus (PVN), medial amygdala, and lateral septum. However, the magnitude of c-fos induction in cortical and hippocampal regions was substantially lower in proestrous and estrous females compared with males and diestrous females. Sex- and estrus cycle-related changes are region specific, as no difference in c-fos induction occurred in the hypothalamic PVN, medial amygdala, or ventrolateral septum in any group. Furthermore, induction of c-fos mRNA in limbic cortexes (but not hippocampus) was positively correlated with progesterone and negatively correlated with ACTH levels. Taken together, this study indicates that cortical structures are differentially stress activated in females depending on the phase of the estrous cycle, perhaps in a progesterone-dependent fashion.