The Fontan procedure for hypoplastic left heart syndrome (HLHS) is well established. Multiple surgical techniques including extracardiac conduits and autologous tissue connections have been developed. We reviewed the results of 100 consecutive patients undergoing the lateral tunnel modification of the Fontan procedure at the University of Michigan. A cross-sectional retrospective study was performed for 100 consecutive patients identified in the University of Michigan Congenital Heart Surgery database with the diagnosis of HLHS. All patients had undergone a lateral tunnel Fontan procedure between June 2000 and August 2004. The medical record was reviewed to assess patient, procedural, and morphologic determinants of outcome. Hospital survival was 97% and intermediate-term survival was 96% with a median follow-up time of 34 months. Preoperative mean pulmonary artery pressure, right ventricular end diastolic pressure, aortic cross-clamp time, and tricuspid valve regurgitation were not associated with late right ventricular function or survival. Three patients required takedown of the lateral tunnel Fontan in the early postoperative period. A positive association was found between protein-losing enteropathy and prolonged (>2 weeks) postoperative pleural drainage (p = 0.035). No patient required cardiac transplantation or late intervention on the Fontan pathway. At the time of follow-up, 100% of patients were New York Heart Association class I or II and 90% were in normal sinus rhythm. The lateral tunnel Fontan procedure for HLHS can be performed with acceptable early and intermediate-term risk. There was a low prevalence of late rhythm disturbances and other complications. Protein-losing enteropathy and prolonged pleural drainage were associated.