A flow injection system incorporated with a polycation-sensitive polymeric membrane electrode in the flow cell is proposed for potentiometric determination of heparin. An external current in nano-ampere scale is continuously applied across the polymeric membrane for controlled release of protamine from the inner filling solution to the sample solution, which makes the electrode membrane regenerate quickly after each measurement. The protamine released at membrane-sample interface is consumed by heparin injected into the flow cell via their strong electrostatic interaction, thus decreasing the measured potential, by which heparin can be detected. Under optimized conditions, a linear relationship between the potential peak height and the concentration of heparin in the sample solution can be obtained in the range of 0.1-2.0 U mL(-1), and the detection limit is 0.06 U mL(-1). The proposed potentiometric sensing system has been successfully applied to the determination of heparin in undiluted sheep whole blood.