Among factors contributing to morbidity and failure of the Fontan circulation is the group of events referred to as thromboembolic complications. These events have been variously attributed to low flow states, stasis in the venous pathways, right-to-left shunts, blind cul-de-sacs, prosthetic material, atrial arrhythmias, and hypercoagulable states. Numerous investigations, most retrospective, have been undertaken to characterize thromboembolic events; describe the frequency and circumstances of these occurrences; and relate the risk of these events to patient, surgical, hemodynamic, and hematologic factors. Practices vary widely with respect to strategies of prophylactic anticoagulation in the hopes of minimizing the occurrence and morbidity of thromboembolism after Fontan operations. Review of the literature suggests that the factors associated with thromboembolic events after Fontan operations likely represent a complex field of biologic factors with multiple interactions. It is unlikely that a single agent will represent the solution to this complex problem.