OBJECTIVES: The impact of conotruncal anomalies (CTAs), including tetralogy of Fallot, truncus arteriosus, ventriculo-arterial discordance, double outlet right ventricle (DORV), and interrupted aortic arch type B, on long-term outcomes remains poorly described in the Fontan cohort. We sought to review the outcomes of Fontan patients with conotruncal anomalies in Australia and New Zealand. METHODS: We reviewed the data from 1835 patients who underwent a Fontan operation between 1975 and 2023 from the Australia and New Zealand Fontan Registry. RESULTS: Conotruncal anomalies occurred in 895 patients (49%), including D-TGA (n = 476), DORV (n = 360), and L-TGA (n = 170). Patients with CTAs had more heterotaxy syndrome (11.3% vs 6.8%, p <
0.001) and less left-ventricular dominance (53% vs 60% p = 0.011). Median follow-up was 11.7 years (IQR: 5.3-20.3 years).). Overall transplant-free survival and freedom from Fontan failure was 84% (95% CI: 81-87%) and 72% (95% CI: 68-75%) at 20 years, respectively. No difference was demonstrated in survival or freedom from Fontan failure between patients with or without CTAs (p = 0.50 and p = 0.83). Pacemaker implantation was more common in patients with CTAs (11.2% vs 8.3%, p = 0.038). Overall, 45 patients underwent outflow tract reinterventions, including semilunar valves, after Fontan operation. Freedom from these reinterventions was 95% (95% CI: 93-96%) at 30 years and was higher in patients with CTAs (p <
0.001). CONCLUSIONS: Patients with conotruncal anomalies did not have a demonstrable difference in long-term survival and freedom from Fontan failure to other patients undergoing Fontan operation. Patients with conotruncal anomalies have higher incidence of outflow tract reinterventions, including semilunar valves, and higher rate of pacemaker implantation.