A method of percutaneously removing a thrombus from a blood vessel by using catheters and thrombus removing system for executing the method. A guide wire catheter includes a first balloon inflatable for blocking the blood vessel at a position downstream of the thrombus. A suction catheter includes a second balloon inflatable for substantially blocking the blood vessel at a position upstream of the thrombus. A thrombus dissolving agent is supplied to a position between the first and second balloons, and dissolved thrombus is drawn through the suction catheter out of the body. An expansion catheter having a third balloon is used to expand, while allowing blood flows, a location of stricture remaining after removal of the dissolved thrombus.