Objectives: To determine the anatomical characteristics of systemic venous collaterals formed after the Fontan operation, and the efficacy of a transcatheter strategy for management. Methods: We reviewed retrospectively the data from cardiac catherization of 50 persistently cyanotic patients after the Fontan operation. Results: A total of 54 transcatheter interventions were performed, at a mean age of 6.3 ± 3.5 years, a mean interval of 2.7 ± 2.9 years from completion of the Fontan circulation. Of 38 patients who had fenestration of the baffle at the time of surgery, 25 had patency of the fenestration, and 24 had the fenestration occluded with a device at the time of interventional treatment for associated venous collaterals. We identified a total of 68 systemic venous collateral channels, of which 36 (53%) were supracardiac, 12 (18%) cardiac, and 20 (29%) infracardiac in origin. The most common site of origin was the brachiocephalic vein (44%), followed by the left phrenic vein (25%). A longer time from surgery, at 3.3 ± 3.4 years, was associated with the identification of collaterals having a diameter larger than 4 mm (p < 0.01). The mean pulmonary arterial pressure was higher in those with larger compared to those with smaller collaterals (13.3 ± 2.8 versus 11.1 ± 2.0 mmHg, p < 0.01). Coils were used for occlusion of 61 vessels, and a Rashkind™ occluder for the remaining 7. After exclusion of the patients undergoing simultaneous closure of their fenestration, systemic saturation of oxygen increased from 89 ± 6% to 95 ± 3% (p < 0.01). Conclusion: Venous collateral channels are common in patients suffering progressive cyanosis in the setting of the Fontan circulation. The collaterals increase in size with time, and are associated with higher pulmonary arterial pressures. Transcatheter treatment is feasible, and results in resolution of cyanosis. Only continuing follow-up will show whether further collateralization occurs in time.