BACKGROUND The Fontan operation (modified from its original version) affords excellent palliation for many patients with various forms of anatomic or functional single ventricle. The purpose of this study was to evaluate the outcome of our experience with the Fontan procedure in Greece. METHODS Fifty-eight consecutive patients with single ventricle physiology had a modified Fontan operation between 1997 and 2009. Their records were reviewed retrospectively. Follow up, which included clinical evaluation and echocardiographic functional assessment, was complete. RESULTS Median age at operation was 5.7 years (range 3 years to 29.4 years); 46.5% had multistage palliation (stage I and II); 79% had prior bidirectional cavopulmonary shunt (stage II) and 8.6% single stage Fontan. Fifty-four patients had an extracardiac conduit total cavopulmonary connection (EC-TCPC) and 4 an intra-atrial lateral tunnel (LT-TCPC). Fenestration was performed in 26 (44.8%) patients. Operative mortality was 0%. One patient required a short period of extracorporeal membrane oxygenator support. The most frequent complication was prolonged pleural effusion. Median duration of pleural effusion was 17 days (range 6-47 days). Median duration of follow up was 5.44 years (range 0.36 to 11.5 years). There were 2 late deaths (overall mortality 3.4%). One patient died from progressive deterioration of ventricular function within 2 years of operation and the other from fulminant endocarditis. Ten subjects have undergone device closure of a persistent fenestration. All 56 surviving patients are in excellent clinical condition (NYHA class I or II). CONCLUSIONS We have performed the Fontan procedure over a period of 13 years in Greece with excellent mid- and long-term results. Longer follow up will be necessary to assess the possible incidence of late severe complications, some of which may necessitate heart transplantation.