Objective: To compare outcomes of extracardiac conduit and lateral tunnel Fontan connections in a single institution over a concurrent time period. Methods: Between January 1994 and September 1998, 60 extracardiac conduit and 47 lateral tunnel total cavopulmonary connections were performed. Age, sex, and weight did not differ between the 2 groups. Compared with the lateral tunnel group (LT group), patients undergoing the extracardiac conduit procedure (EC group) had a trend to a higher incidence of morphologically right ventricle (EC group 48% vs LT group 32%; P < .09), a higher incidence of isomerism/heterotaxy syndrome (EC 22% vs LT 0%; P < .001), worse atrioventricular valve regurgitation (EC 11% moderate-plus vs LT 0%; P < .06), and lower McGoon indices (EC 1.8 ± 0.5 vs LT 2.1 ± 0.5; P < .03). Preoperative arrhythmias, transpulmonary gradients, room air oxygen saturations, ejection fractions, ventricular end-diastolic pressure, and pulmonary artery distortion did not differ between groups. Cardiopulmonary bypass times and fenestration usage were similar in both groups. Results: Overall operative mortality was 5.6% and did not differ between groups. The LT group had a significantly higher incidence of postoperative sinoatrial node dysfunction (45% vs EC group 15%; P < .007), supraventricular tachycardia (33% vs EC group 8%; P < .0009), and need for temporary postoperative pacing (32% vs 12%; P < .01). Median duration of intensive care unit stay (EC 2 days, range 1-10 days, vs LT 2.8 days, range 1-103 days; P < .07) and ventilatory support (EC 1 day, range 0.25-10 days, vs LT 1 day, range 0.25-99 days; P < .03) were all longer in the LT group. Median chest tube drainage (EC 8 days, LT 9 days) was similar in both groups. Follow-up averaged 2.5 ± 1.4 years in the EC group and 2.8 ± 1.9 years in the LT group. There were 2 late deaths. Overall survival is 94% at 1 month, 92% at 1 year, and 92% at 5 years. Late ejection fraction or atrioventricular valve function did not differ between groups. Intermediate follow-up Holter analysis showed a higher incidence of atrial arrhythmias in the LT group (23% vs 7%; P < .02). Multivariable analysis showed that (1) prolonged cardiopulmonary bypass time was the only independent predictor for perioperative mortality, prolonged ventilation and intensive care unit length of stay, and increased time to final removal of chest tube drains and (2) lateral tunnel Fontan connection is an independent predictor of early postoperative and intermediate atrial arrhythmias. Conclusions: Although patients in the EC group were at higher preoperative risk, their outcomes were comparable with those of the LT group. Use of the extracardiac conduit technique for the modified Fontan operation reduces the risk of early and midterm atrial arrhythmia.