Since 1983, when c-DNA was isolated, recombinant tissue plasminogen activator (rtPA), an endothelial-cell-produced activator of fibrinolysis is used, more increasingly often in therapy of thrombosis. Whereas some studies have been published regarding efficacy and safety rtPA in different thrombotic states of adults, only case reports exist in children. Doses vary widely (0.8-6 mg/kg/d), bleeding complications are reported in up to 50%. We report on four infants with complex cyanotic congenital heart disease who developed an early post-operative thrombosis of a modified Blalock-Taussig shunt. By local low dosage application of rtPA we could achieve a complete lysis of the thrombus in three of our four patients. In one patient we were unsuccessful due to a distal stenosis of the shunt. This infant required repeat surgery with creation of a central aortopulmonary shunt. We saw severe bleeding in one, requiring transfusion of packed cells, and formation of a perigraft reaction in another patient. In our experience local application of rtPA in low doses is a good therapeutical option in patients with thrombosis of aorto-pulmonary shunts, especially in the first postoperative days.