Most of the biological effects of estrogens are mediated via the estrogen receptors (ERs) at the level of gene regulation. Recently, new information regarding the role of ERs in physiology, pathology and the mechanisms through which estrogens bring about these functions has emerged. The physiological effects of estrogen are manifested through two ER isoforms - ERα and ERβ - which display distinct regions of sequence homology. The crystal structures of these receptors bound to their specific ligands (e.g. agonists or antagonists) have revealed much about how ligand binding alters receptor structure/conformation and the interaction with coactivators or corepressors as well as how it determines the cellular response to a ligand. ERs are involved in the variety of physiological and pathological activities and different cells and tissues have shown divergent responses to these two receptor isoforms. The discovery of sub-isoforms of ER alpha and beta has further complicated our understanding of how the interaction between ERs and its ligands contribute to the development of disease. Nevertheless, continuing efforts in the study of ERs have helped us to more clearly define their role in disease and to develop novel, ER-targeted therapeutics.