The frequency of thromboembolism after the Fontan procedure has not been specifically addressed. Seventy patients underwent this operation between 1987 and 1992, and complete information was available on 64. Forty-five had a right atrium-pulmonary artery anastomosis, 17 had a total cavopulmonary connection, and 2 had a right atrium-right ventricle anastomosis. No patient received anticoagulants for more than 8 months postoperatively. Seven patients died in the early postoperative period (< 30 days). Ten cases of thromboembolism were identified in the follow-up, which ranged from 6 to 55 months (mean follow-up, 24.5 +/- 17 months). They occurred 7 days to 4.5 years after the Fontan repair. Seven thombi were on the systemic venous or pulmonary aspect of the circulation and three, on the systemic arterial aspect. Freedom from thromboembolism was 75% at 4 years. We conclude that thromboembolism is common after the Fontan procedure; it can occur several days to years postoperatively; it is an important cause of morbidity; and it may partly explain late death after the Fontan operation. Our data suggest that all patients undergoing this procedure require long-term anticoagulant therapy.