A variety of compounds, including the selective estrogen receptor (ER) modulators tamoxifen and raloxifene, phytoestrogens such as genistein, and xenoestrogens such as bisphenol, bind to the estrogen receptor and elicit biological responses. Structural studies have linked the altered activity of compounds such as 4-hydroxytamoxifen, raloxifene, genistein, and tetrahydrochrysene, which have substantially different structures from estradiol (E2), to differences in the positioning of the critical “helix 12” within the ligand-binding domain (LBD) of the ER–ligand complex. However, subtle permutations of the E2 molecule would also be expected to modulate the pattern of responses within a cell. Forty-two ligands were constructed by the addition or relocation of double bonds, hydroxyl, keto, amino, and nitro substituents throughout the estra-l,3,5(10)-triene (estratriene) ring system. In this review, we summarize the effects of subtle changes in the estratriene molecule on the ability of the receptor complex to stimulate the growth of MCF-7 cells, or affect the expression of four estrogen-regulated genes (progesterone receptor, pS2 protein, cathepsin D, and tissue plasminogen activator), as well as undergo nuclear processing and downregulate ERα mRNA. The affinity of these ligands for, and mechanism of their binding with, the ERα have been measured, along with their effect on the conformation of the ER–ERE complex. In particular, two A-ring isomers of E2, 2- and 4-hydroxyestratriene-17β-ol, display gene selective activity within MCF-7 cells which is dependent on complex endogenous promoters, an intact AF-2 and is sensitive to the level of SRC-1. Both of these A-ring isomers function as antiestrogens. Molecular modeling of these two A-ring isomers complexed with the ER ligand-binding domain supports the idea that the conformation of the LBD is affected by subtle changes in the estratriene structure.