Although patients undergoing surgery with the Fontan procedure or its modifications are increasingly recognised to be at risk for thromboembolism, further knowledge is needed to minimise this complication and its sequels. To address this issue, we reviewed 100 patients operated with the Fontan procedure, the bidirectional Glenn anastomosis and/or the total cavopulmonary connection to describe our incidence and clinical characteristics of postoperative formation of thrombus. Symptomatic thrombosis or cerebrovascular accidents were found in 5 patients. Asymptomatic thrombus were found in another 5 patients. Three patients had venous thrombi. In 6 patients the thrombosis was found on the arterial side. In all these cases, the thrombus was located in the stump of the divided pulmonary trunk. In 3 of these patients, sudden onset of hemiparesis preceded the diagnosis of the thrombus while the remaining 3 patients were asymptomatic. In 3 cases, the formation of thrombus in the stump of the divided pulmonary trunk occurred after a bidirectional Glenn anastomosis. One patient developed severe neurological symptoms 2 months after a total cavopulmonary connection. No thrombus was found, but the patient had a small right-to-left shunt and embolization could not be excluded. The incidence of thrombosis after Fontan-type surgery in this study is 10%. Although not all episodes of thrombosis are symptomatic, there is a significant risk of severe sequels due to embolization to the pulmonary or cerebral circulations. The stump of the divided pulmonary trunk is one of the main sites for intracardiac formation of thrombus, even after a bidirectional Glenn anastomosis.