This is a unique report of systemic-to-pulmonary artery shunt thromboses secondary to primary antiphospholipid syndrome and antithrombin III deficiency in a neonate with cyanotic congenital heart disease. This infant with tricuspid atresia experienced thromboses of two modified Blalock-Taussig shunts en route to a bidirectional cavo-pulmonary shunt and potential future Fontan operation. Chronic warfarin anticoagulation has prevented additional thrombo-embolic events.