Estrogen receptors (ER) and (ER) have distinct functions and differential expression in certain tissues. These differences have stimulated the search for subtype-selective ligands. Such ligands offer the potential to target specific tissues or pathways regulated by one receptor subtype without affecting the other. As reagents, they can be utilized to probe the physiological functions of the ER subtypes to provide information complementary to that obtained from knockout animals. A fluorescence resonance energy transfer (FRET) assay was used to screen a 10,000 compound chemical library for ER agonists. From the screen, we identified a family of ER-selective agonists whose members contain bulky oxabicyclic scaffolds rather than the planar scaffolds common to most ER ligands. These agonists are 10 to 50-fold selective for ER in competitive binding assays and up to 60-fold selective in transactivation assays. The weak uterotrophic activity of these ligands in immature rats and their ability to stimulate expression of an ER regulated gene in human U2OS osteosarcoma cells provides more physiological evidence of their ER- selective nature. To provide insight into the molecular mechanisms of their activity and selectivity, we determined the crystal structures of the ER ligand-binding domain (LBD) and a peptide from the glucocorticoid receptor interacting protein 1 (GRIP1) coactivator complexed with the ligands, OBCP-3M, OBCP-2M and OBCP-1M. These structures illustrate how the bicyclic scaffolds of these ligands are accommodated in the flexible ligand-binding pocket of ER. A comparison of these structures with existing ER structures suggests that the ERbeta selectivity of OBCP ligands can be attributed to a combination of their interactions with Met-336 in ER and Met-421 in ER. These bicyclic ligands show promise as lead compounds that can target ERbeta. Our understanding of the molecular determinants of their subtype selectivity provides a useful starting point for developing structurally similar ER modulators.