Transcatheter fenestration and balloon dilation of an atrial baffle created from native atrial tissue was attempted in a 15-year-old girl with failing Fontan physiology and protein-losing enteropathy. After transseptal puncture, initial dilations with a 10-mm and 12-mm diameter balloon resulted in an inadequate fenestration, with no significant decrease of right atrial pressure or systemic arterial saturation. Dilation of the fenestration with a 16-mm-diameter balloon produced a tear of the atrial septum and subsequent death. Balloon dilation of native atrial tissue may result in uncontrolled tears of the atrial septum.