In a search for new ligands selective for the estrogen receptor beta (ERbeta), we prepared a series of non-steroidal compounds having an isocoumarin core structure. An interesting feature of these derivatives is that they bear the same functionalities as the well-known ERbeta -selective, isoflavone phytoestrogens daidzein and genistein, but in an isomeric arrangement. These compounds could be prepared efficiently by electrophilic cyclization of acetylenic ester precursors, followed by simple manipulations to introduce additional substituents. Through a reduction of some of the isocoumarins, we also obtained isomeric analogs of the isoflavone metabolites equol and dehydroequol. The compounds we prepared were evaluated in ER binding assays, and selected compounds were studied further in cell-based gene transcription assays. Several of the isocoumarins and their analogs are high-affinity ligands that show considerable selectivity for ERbeta in terms of binding affinity, and strikingly high ERbeta selectivity in terms of potency in gene transcription assays. Two of the best compounds, which combine high transcriptional potency with an ERbeta selectivity greater than 1000, should prove to be excellent probes of ERbeta function in vivo.