Sex differences in the activity of the hypothalamus-pituitary-adrenal (HPA) axis in rats are programmed by neonatal estrogens; exposure of female neonates to estradiol (E2) leads to overt defeminization of endocrine and behavioral functions in adulthood. E2 activates both estrogen receptor isoforms (ERa and ERb); these are widely expressed in the brain, and differentially regulate HPA axis activity in adulthood. However, the contributions of each ER isoform to the sex-specific organization of the neural mechanisms governing HPA axis function remain unknown. ERa, ERb agonists (PPT and DPN, respectively) or E2 were administered to female rats on days 1-10 of life. Animals subsequently underwent endocrine (HPA axis and reproductive) and behavioral profiling (anxiety-related and reproductive) in adulthood, and patterns of expression of relevant genes were monitored in limbic structures post mortem. Exposure of neonatal females to PPT or DPN led to distinctly different HPA secretory profiles, neither of which completely recapitulated the effects of E2. Thus, whereas impaired glucocorticoid negative feedback was the most prominent effect of PPT treatment, increased basal corticosterone secretion was the most obvious characteristic of DPN-treated animals. Behavioral analysis revealed higher anxiety levels in PPT-treated animals, similar to those observed in E2-treated female neonates and control males; in contrast, DPN treatment was associated with reduced anxiety-like behavior. Parallel treatment-specific alterations in the expression of the genes encoding mineralocorticoid (MR) and glucocorticoid (GR) receptors in the hippocampus and amygdala and altered expression of ERb mRNA in discrete brain regions, as well as disturbed ovarian activity, were also found; together, they suggest potential mechanisms that could account for the different endocrine and behavioral phenotypes observed. Defeminization of HPA axis activity and associated anxiety-related behavior depends on balanced activation of ERa and ERb during early postnatal life, rather than on the activation of a specific ER isoform. Long-term E2-, PPT- and DPN-induced alterations in the expression levels of GR and MR in the hippocampus and amygdala, as well as disrupted ovarian activity appear to be largely responsible for eliciting and maintaining the aberrant endocrine and behavioral phenotypes induced by estrogenization of neonatal females.