Specific congenital heart anomalies significantly increase the risk for late atrial arrhythmias, raising the question whether prophylactic arrhythmia operations should be incorporated into reparative open heart procedures. Currently no consensus exists regarding standard prophylactic arrhythmia procedures. Questions remain concerning the arrhythmia-specific lesions to perform, energy sources to use, need for atrial appendectomy, and choosing a right, left, or biatrial Maze procedure. These considerations are important because prophylactic arrhythmia procedures are performed without knowing if the patient will actually experience an arrhythmia. This review identifies congenital defects with a risk for the development of atrial arrhythmias and proposes standardizing lesion sets for prophylactic arrhythmia operations.