Transcatheter fenestration to create an interatrial communication has been used to treat patients with protein losing enteropathy (PLE) after Fontan operation. No systematic data have been reported assessing the results of this procedure. Our institutional database was queried to identify patients after Fontan operation who had transcatheter fenestration to treat PLE. Clinical notes, laboratory data, echocardiograms, and cardiac catheterization data were reviewed. From 1995 to 2005, 16 transcatheter fenestration procedures were performed in seven patients. Median age at fenestration was 18 years (range 13–41 years). Median duration of follow-up was 3.6 years (range 0.2–10.4 years). Techniques for fenestration included blade/balloon septostomy, stent placement, Amplatzer-fenestrated ASD device, and balloon dilation of previous stent. Size of the fenestration created was 5.2 ± 1.1 mm. Systemic venous pressure remained unchanged after fenestration. Cardiac index increased significantly. Reduction of ascites and edema was noted after 9 of the 16 procedures. Ten of 16 (63%) of fenestrations spontaneously occluded. Three patients are free of ascites although recurrence of PLE occurred in all. One patient with a patent fenestration continues to have ascites. Two patients had Fontan takedown. One patient had conversion to a fenestrated extracardiac conduit Fontan and died postoperatively. The results of transcatheter Fontan fenestration are often disappointing. Maintaining fenestration patency is difficult. Even after “successful” fenestration, resolution of PLE may be incomplete and recurrences have occurred in all. Early consideration should be given to Fontan takedown or cardiac transplant in severely symptomatic patients with PLE who do not respond to fenestration. Transcatheter fenestration may be a bridge to a definitive procedure.