OBJECTIVES The study was done to determine the prevalence of pulmonary emboli (PE) in asymptomatic adult Fontan patients and to identify the risk factors associated with PE. BACKGROUND Right atrial thrombi and systemic thromboembolic complications have been reported after the Fontan procedure. However, the frequency of silent PE in this patient population is not known. METHODS All consecutive adult Fontan patients attending the adult congenital clinic over a six-month period underwent ventilation-perfusion (VQ) scanning and blood testing for thrombophilia tendency. If the VQ scan showed an intermediate or high probability for PE, a computerized tomography (CT) pulmonary angiogram was performed to confirm the presence of PE. RESULTS Thirty patients (mean age 26 +/- 7 years, 57% men) were included in this study. Five (17%) adult Fontan patients had an intermediate or high probability for PE on VQ scan, all of which were confirmed on CT pulmonary angiography. No patient had a thrombophilia tendency. Pulmonary emboli were not present in any patients (30%) taking warfarin. Late age at time of Fontan operation (19 +/- 6 years vs. 11 +/- 6 years, p = 0.012) and type of Fontan anatomy (p = 0.001) were associated with increased risk of silent PE. CONCLUSIONS Seventeen percent of adult patients with Fontan procedure have clinically silent PE. The long-term hemodynamic implications of this with respect to Fontan attrition over time are unknown. Large randomized prospective studies looking at anticoagulation therapy in all Fontan patients are urgently needed.