Background: Thrombosis in the systemic circulation is a rare but hazardous complication in patients with single ventricle physiology. Methods: We evaluated the clinical significance of thrombosis in the systemic circulation and the necessity of removal by retrospective review of medical records in the Seoul National University Children���s Hospital. Results: Six patients were confirmed to have thrombosis in the proximal PA stump and 2 patients in rudimentary ventricle by cardiac CT. The age at the diagnosis of thrombosis was from 0.6 to 18.5 years old (mean age: 11.9 year-old). In PA stump thrombosis patients, thrombosis was found at mean 9.6 years after main PA ligation (range: 0.1 - 15.1 years). Three patients underwent initial palliative PA banding and three patients Blalock-Taussig shunt operation. Five among 8 patients were taking aspirin and 1 patient warfarin at the time of thrombus diagnosis. Two patients showed mild liver cirrhosis by liver CT, but did not have coagulopathy. All the patients did not have associated thrombosis at the venous side. On brain MRI, three patients showed cerebral infarction and one patient showed suggestive old ischemia. Three patients with PA stump thrombus underwent PA stump thrombectomy and pulmonary valve obliteration. One patient who showed thrombosis immediately after BCPS operation underwent concomitant pulmonary valve closure during Fontan operation. One patient with thrombus in rudimentary ventricle underwent VSD closure with thrombectomy. We did not treat 2 patients with PA stump thrombus by cardiac CT, because we could not find any thrombus shadow by echocardiography. Conclusion: We should not overlook the possibility of thrombus in ligated PA stump with or without pulmonary regurgitation and rudimentary ventricle, which may raise a risk of embolic stroke in the patients with single ventricle physiology. Empirical pulmonary valve obliteration at the time of PA ligation to reduce the risk of later thrombus formation and aggressive thrombectomy in case of thrombosis in the proximal PA stump and rudimentary ventricle should be considered in this patient group.