The habenular complex is involved in several estrogen-dependent reproductive behaviors in female rats, namely, sexual behavior, maternal behavior, and postpartum sexual behavior. Although it is known that estrogen acts in other brain regions to mediate these behaviors, it is not known whether estrogen may also act directly on the habenular complex. To address this possibility, we examined this region for the presence of estrogen receptor (ER). This analysis was carried out in separate experiments by using in situ hybridization, immunocytochemistry at the light and electron microscopic levels, and steroid autoradiography. Neurons within the lateral habenula (LHb), but not the medial habenula, express ER mRNA, contain ER immunoreactivity (ER-ir) in their nuclei, and concentrate radiolabelled estradiol, providing strong evidence for the presence of functional ER in the lateral habenula. There were also ER-ir containing punctate fibers within the LHb, which, at the electron microscopic level, in part, proved to be axons and presynaptic axonal terminals. Both the level of ER-ir in cell nuclei and the density of ER-ir fibers within the LHb were regulated during the course of pregnancy and the postpartum period, suggesting that the sensitivity of the LHb to estrogen may be altered during this time. Taken together, these results demonstrate that the LHb is likely a more estrogen-sensitive region than was previously considered, and they suggest alternative mechanisms of action for ER. ER within the LHb may play a critical role in the involvement of the LHb in estrogen-dependent female reproductive behaviors.