Thrombus removal apparatus includes a balloon catheter with a short balloon at a distal end thereof. An aspiration catheter is disposed coaxially over the balloon catheter. The balloon catheter includes a plurality of holes for the administration of lytic agent. The apparatus does not seal off completely the zone of the vessel around the thrombus, thereby allowing movement of blood within the vessel. The balloon is shaped so that it can be pulled along the vessel in an upstream direction so as to drag against the vessel walls for assisting in the removal of the thrombus.