BACKGROUND: The Fontan circulation is associated with an increased risk of thromboembolic events (TEs). As many as 25% of these thrombotic events result in fatality. More subtle adverse effects on the pulmonary circulation from embolic thrombi may further impair adequate functioning of the circuit. Despite these well-documented phenomena, the most optimal approaches to thromboprophylaxis are still not clearly defined. OBJECTIVE: A meta-analysis of published trials in English on PubMed and Cochrane libraries that evaluated the role of using TE prophylaxis in patients who underwent the Fontan procedure was conducted. METHODS: 10 studies with a total number of 1200 patients with an average follow-up time of 7.1 years were identified. A random effect model was used. RESULTS: The incidence of TE was significantly less in patients who received TE prophylaxis (using either aspirin or warfarin) compared with patients who did not receive TE prophylaxis (OR 0.425, 95% CI 0.194 to 0.929, p<0.01, I=37%). The incidence of TE was significantly lower in patients who received aspirin compared with no TE prophylaxis (OR 0.363, 95% CI 0.177 to 0.744, p<0.01, I=0%) and who received warfarin compared with no TE prophylaxis (OR 0.327, 95% CI 0.168 to 0.634, p<0.01, I=2.5%). There was no significant difference in incidence of TE between warfarin and aspirin (OR 0.936, 95% CI 0.609 to 1.438, p=0.54, I=0%). Furthermore, there was no significant difference in incidence of early TE (within 6 months of the operation) or late TE (>6 months) between patients receiving warfarin and aspirin (OR 0.784, 95% CI 0.310 to 1.982, p=0.37, I=8%) and (OR 0.776, 95% CI 0.249 to 2.42, p=0.3, I=45%), respectively. When only total cavopulmonary connection patients were included, there was again no difference between warfarin and aspirin in the incidence of TE (OR 0.813, 95% CI 0.471 to 1.401, p=0.34, I=11%). CONCLUSIONS: This study shows a significantly lower incidence of TE after Fontan procedure if either aspirin or warfarin is used. This meta-analysis suggests no significant difference in incidence of early or late TE in patients receiving aspirin compared with warfarin.