In the transplanted heart with biatrial anastomosis, atrial flutter is common and is amenable to catheter ablation. Although this arrhythmia is isthmus dependent, the unique atrial architecture with a suture line through the inferior vena cava-tricuspid annulus isthmus makes the substrate atypical. A cardiac transplant recipient with atrial flutter underwent successful catheter ablation. Five weeks after the procedure, the patient died of a myocardial infarction. The autopsy and histological findings are described and correlated with the electroanatomic map obtained during the ablation. Due to the atrial suture lines, atrial flutter following cardiac transplantation is an isthmus dependent arrhythmia with a different arrhythmogenic substrate. The electrical isthmus (atrial tissue from the tricuspid annulus to the suture line) in these hearts is smaller than the anatomic isthmus.