Severe thromboembolism occurred in 3 of 37 patients who had undergone Fontan-type operations for correction of congenital heart defects several months to years after the operation. The patients were screened for coagulation factor abnormalities to find out whether known prothrombotic risk factors could explain the high frequency of thromboembolism. 63 abnormalities were found in 24 of the 37 patients. The commonest and most pronounced abnormality was deficiency of protein C, a known risk factor. Concentrations of antithrombin III and factors II and X were significantly lower in protein-C-deficient patients than in those with normal protein C concentrations. These findings suggest that the high thrombotic risk in these patients is caused or at least associated with an imbalance between procoagulant and anticoagulant factors.