Genistein (5,7,4'-trihydroxyisoflavone) modulates the function of several transmembrane ion-channel proteins by mechanisms that are unrelated to phosphorylation events. Daidzein (7, 4'-dihydroxy-isoflavone) typically exhibits modest effects, whereas genistin (7-O-glucosyl-genistein) usually exhibits no effect on ion-channel activities. Genistein appears to modulate gramicidin A ion channels by alteration of bilayer mechanical properties, but the associated molecular interactions have not been defined. The incorporation of daidzein into phosphatidylcholine liposomes promotes aggregation and precipitate formation which is problematic for structural studies based on NMR spectroscopy. In the present study, daidzein was incorporated into sodium dodecyl sulfate (SDS) micelles to provide a stable system with no evidence of micelle aggregation. For this reason genistein, daidzein, genistin, and osajin (a diprenyl-genistein derivative) were incorporated into SDS micelles (in D2O) to evaluate differences in position and orientation within micelle structures. The H-1 NMR line widths, as a function of Mn2+ concentration, indicate that genistein is quite mobile and buried within the hydrophobic micelle core. Daidzein and genistin also are mobile but exhibit average positions near the micelle/aqueous interface, with polar groups oriented toward the aqueous compartment. These results demonstrate that daidzein, with only two hydroxyl substituents, has a greater affinity for a polar environment than genistein with three hydroxyl substituents. The 5-hydroxyl group of genistein forms an intramolecular hydrogen bond with the 4-carbonyl group, which diminishes the molecular affinity for a polar matrix. These results suggest an explanation for the relative abilities of these compounds to increase gramicidin channel lifetimes and modulate other ion-channel types.