Inwardly rectifying potassium channels play an important role in the maintenance of membrane potential in neurons and myocardium. Identification of functional regulation mechanisms concerning these channels may lead to the development of specific modulators for these channels. Genistein is an isoflavone with potent inhibitory activity on protein tyrosine kinase. In this study, we have found that among three members of the Kir family (Kir2.3, Kir2.1, and Kir3.4* [a highly active mutant of Kir3.4, Kir3.4-S143T]) we tested, genistein significantly inhibited Kir2.3 currents. Using the two-electrode voltage clamp technique, we have demonstrated that micromole concentrations of genistein concentration-dependently and reversibly inhibited the currents of Kir2.3 channel expressed in Xenopus oocytes with an IC50 of 16.9+/-2.8 microM. Using the whole-cell patch-clamp technique, genistein also inhibited the currents of Kir2.3 channel expressed in HEK293 cells with an IC50 of 19.3+/-3.2 microM. Genistein had little or no effect on Kir2.1 and Kir3.4* currents. The effect of genistein on Kir2.3 currents was not affected by vanadate, a potent protein tyrosine phosphatase inhibitor. Furthermore, the effect of genistein was not mimicked by daidzein, an inactive analogue of genistein, or another potent tyrosine kinase inhibitor, tyrphostin 23. Chimeras between Kir2.3 and Kir2.1 channels were constructed to identify molecular basis that distinguished the effect of genistein on these channels. It was found that the transmembrane domains and the pore region of Kir2.3 channel were important determinant for high sensitivity for genistein inhibition.