A young i.v. drug abuser presented with an extensive iliofemoral deep vein thrombosis and signs of severe sepsis. Subsequent investigations revealed multiple septic emboli in his lungs originating from infected thrombus in his leg. Despite systemic anti-coagulation and appropriate parenteral antibiotics, he continued to show signs of worsening acute infection. Percutaneous mechanical thrombectomy was performed successfully and resulted in an immediate improvement in his condition. In this report, we discuss the novel use of this technique for source control in a patient with septic shock secondary to infected thrombus.