A system for mechanically capturing and removing a thrombus from a blood vessel includes a flexible guidewire adapted to contact the thrombus in the blood vessel, an aspiration catheter, an elongate catheter, and a self-expanding body fixedly attached to a distal end portion of the elongate catheter. The self-expanding body extends distally from the elongate catheter for capturing the thrombus. The self-expanding body preferably has a proximal end portion with a tapered shape and an open distal end. The self-expanding body is permeable for allowing blood to pass through the self-expanding body and into the central lumen of the aspiration catheter. The system may further include a thrombolytic drug to help dissolve the thrombus before capturing the thrombus with the self-expanding body.