Thrombosis of central veins has become more prevalent because of increased use of long-term central venous catheterization. Candida superinfection of the thrombus can occur particularly in patients on long-term antibiotic therapy and on parenteral nutrition. Removal of the catheter, thrombolytic therapy, anticoagulation, and antifungal therapy with amphotericin B will usually eradicate the candidemia and restore venous patency. Occasionally this therapeutic regimen fails. This case report illustrates such a failure in which multiple pulmonary emboli could have caused death. Surgical thrombectomy of the innominate vein effectively removed the source of the Candida sepsis and maintained patency of a major vein. Thrombectomy should be considered as a therapeutic option in septic central vein thrombosis.