In the setting of functional single ventricle with pulmonary overcirculation, pulmonary artery banding is frequently used to alleviate symptoms and to prepare for staged repair. At subsequent cavopulmonary anastomosis or Fontan procedure, the pulmonary artery may be ligated at the site of the pulmonary band. This article describes the association of embolic stroke and thrombus in a ligated or divided pulmonary artery stump in three patients with functional single ventricle. These events occurred from 1990 through 1992 among the 1700 inpatient pediatric cardiology admissions at two institutions. The patients, ranging in age from 15 months to 9 years, had cerebral infarctions documented by computed axial tomography scan or magnetic resonance imaging associated with the echocardiographic finding of thrombus in the proximal pulmonary artery stump after the embolic strokes. The strokes occurred 5 days to 5 years after surgery. Two patients had a second infarction within 2 to 5 weeks of the initial stroke. It is concluded that the presence of the ligated pulmonary artery stump may place patients at risk for embolic stroke. Surgical approaches to reduce the risk of thrombus formation should be considered prospectively in this patient group.