The purpose of this study was to determine the effects of newer Fontan modifications (lateral tunnel with or without fenestration) and patient's age at surgery on the incidence and impact of symptomatic postoperative early and intermediate arrhythmias. Modifications to the Fontan procedure are used to decrease postoperative complications, and the Fontan procedure is now being performed on younger patients to reduce age-related changes in ventricular function. A retrospective review was done of the medical records of 151 consecutive patients, ranging in age from 1 to 49 years, who underwent a Fontan procedure at Texas Children's Hospital between 1987 and 1993. Risk factors were identified for early and intermediate arrhythmias. Age at time of the procedure was an independent predictor of early atrial arrhythmias (p = 0.03), ventricular arrhythmias (p = 0.003), and junctional ectopic tachycardia (JET) (p = 0.05). We found that the older the patient at surgery, the higher the incidence of atrial and ventricular arrhythmias, whereas the younger the patient, the higher the incidence of JET. Using Cox's proportional-hazards model, the risk of intermediate atrial arrhythmias after lateral tunnel modification was 1/3 that after atriopulmonary connection. Younger patients who underwent the Fontan procedure had a lower risk for early atrial and ventricular arrhythmia but an increased risk for JET. The lateral tunnel modification can be performed in order to reduce the risk of intermediate atrial arrhythmias.