Three biological activities of 12 soy isoflavones were investigated in terms of the structure-activity relationship. Seven molecular descriptors and one absorption predictor were significantly related to the inhibition of cytochrome P4501 activity in HepG2 cells by soy isoflavones, yielding water solubility [correlation coefficient (gamma)=-0.779] and hydrophobicity (gamma=0.718) as more relevant molecular properties. By contrast, the inducing activities of 12 soy isoflavones both on quinone reductase in HepG2 cells and proliferation of the osteoblastic MG-63 cells demonstrated significant correlation to the hydroxyl and methoxyl substituents on the isoflavone skeleton (p < 0.01).