Objectives: This study aims to compare the outcome of the two co-existing modifications of staged total cavopulmonary connection (TCPC) the intra-atrial lateral tunnel (ILT) and the extracardiac conduit (ECC). Methods: We included 209 patients after staged TCPC (102 ILT and 107 ECC), operated on between 1988 and 2008. Medical and surgical records were reviewed for (1) patient demographics and cardiac anatomy; (2) pre-Fontan procedures; (3) pre-Fontan haemodynamics and cardiac functional status; (4) operative details; (5) postoperative hospital course; (6) follow-up information on arrhythmias and thrombo-embolic events; (7) post-Fontan interventions; and (8) clinical status at last follow-up until June 2008. Results: Median follow-up duration was 4.3 years (interquartile range 1.5-7.4 years). At 6-year follow-up, freedom from Fontan failure (i.e., mortality or re-operations for Fontan failure) was 83% for the ILT and 79% for the ECC groups (p=0.6); freedom from late reoperations (other than re-operations for Fontan failure) was 79% for the ILT and the ECC groups and freedom from arrhythmias was 83% for the ILT, and 92% for the ECC groups (p = 0.022). Multivariable Cox regression analysis identified intensive care unit stay and cardiopulmonary bypass time as risk factors for Fontan failure, but they were not strong predictors. Right ventricular morphology was identified as a risk factor for arrhythmias. The occurrence of thrombo-embolic events was low with no difference between the ILT and the ECC groups, and irrespective of the postoperative use of anticoagulant or anti-platelet aggregation therapy. At most recent follow-up, sinus rhythm was present in 70% of patients; in 23% of the patients, ventricular function was found to be moderately or severely impaired at echocardiography. Conclusions: Outcome after staged ILT- and ECC-type Fontan operations is good, with comparable freedom from late re-operations and freedom from Fontan failure at 6-year follow-up. The incidence of arrhythmias was significantly lower in the ECC group. Right ventricular morphology was identified as a risk factor for arrhythmias. (C) 2009 European Association for Cardio-Thoracic Surgery. Published by Elsevier B.V. All rights reserved.