The effect of a polyanionic variably substituted sulfobutyl ether-b-cyclodextrin (SBE-b-CyD), complexation on the UV absorption of genistein (Gen) and daidzein (Dai) was studied in pure water. A phase solubility study was performed, according to the method reported by Higuchi and Connors, to evaluate the changes of isoflavones in the complexation state and type-A L solubility diagrams for both isoflavones were obtained suggesting that they form complexes with 1:1 molar ratio. These results were confirmed by Job's plot method. Complexation strongly increases the water solubility of isoflavones. The in vitro dissolution of isoflavones entrapped into SBE-b-CyD significantly surpassed that of the free isoflavones (over 90 % of the loaded Gen and Dai dissolved in 15 and 30 min, respectively). Finally, 1:1 molar ratio solid complexes were prepared by the kneading method and characterized in solid state by FTIR-ATR spectroscopy, with particular regard to O-H and C=O stretching vibrations, achieving structural information on the modifications induced by complexation on the H-bond scheme, also by applying band decomposition and curve-fit.