The structure-activity relationship for genistein to scavenge peroxyl radical was clarified by density functional theory (DFT) calculations using the B3LYP/6-31G(d,p) method. It was revealed that the conjugation of an electron-withdrawing 1,4-pyrone group with A-ring of genistein was not beneficial to enhance the radical-scavenging activities. Thus, hydroxyl in B-ring became the active center of genistein to scavenge peroxyl radical.