Systems and methods for treating thrombosis by driving the drugs or lytic agents through the thrombus by pressure, are disclosed. The system preferably comprises a guide catheter with an occlusion balloon for isolating the region proximal to the thrombus, a guide wire with an occlusion balloon for isolating the region distal to the thrombus and an infusion catheter for delivering drugs or other agents into the region distal to the thrombus under pressure. A lumen of the guide catheter is preferably provided to evacuate material proximal to the thrombus, decreasing the pressure in the proximal to the thrombus. The lumen can be coupled to a thrombus filter to remove thrombolytic material from the drug or lytic agent evacuated from the proximal region. The filtered drug or lytic agent can then be redelivered into the distal region. Recycling of the drug or lytic agent in this manner decreases the costs of the procedure. The systems and methods of the invention can be used to treat other blockages in lumens or vessels in the body or to deliver drugs or other agents to lumens, vessels or cavities within the body, as well.