Apparatus for removing emboli during an angioplasty, stent, or surgical procedure comprising a catheter (11) having an occlusion element (10), an aspiration lumen, a blood outlet port in communication with the lumen, a guide wire (20) having a balloon, a venous return catheter with a blood inlet port (51), and tubing that couples the blood outlet port (48) to the blood inlet port. A blood filter (50), a flow sensor, a flow control valve (175) and/or a pump may also be included in-line with the tubing to better facilitate filtering of emboli from blood reperfused into the patient, to better monitor, and control the degree of flow reversal.