The fenestrated Fontan operation was introduced as a modification of the "completed" Fontan operation for patients with high risk factors, and low operative mortality has frequently been reported. However, use of the umbrella device is now restricted, and this procedure should be performed without subsequent closure. In this paper, we review our clinical experience with this procedure and discuss ongoing problems. Sixteen patients (4 tricuspid atresia and 12 other cardiac anomalies including 5 cases of univentricular heart) underwent the fenestrated Fontan operation (7 atriopulmonary and 9 total cavopulmonary connection). All of them have some risk factors for a completed Fontan operation. There were three early deaths of the 16. Two experienced an anticipated thromboembolic accident, one of which involved the pulmonary aspect while the other involved the arterial aspect. Patients who survived the operation have progressed well and have a clinical status of New York Heart Association class I, with the exception of one late death due to congestive heart failure. There have been no thromboembolic accidents in this group during the late follow-up period. Spontaneous closures of the fenestrations were noted in two patients. The late mean Qp/Qs value in patients with patent fenestrations was 0.80 +/- 0.1, SaO2 was 88.8 +/- 5.6%, and right atrial pressure was 9.7 +/- 3.8 mmHg. No major problems have been encountered in patients with a patent fenestration over extended periods. A modified Fontan operation to fit a permanently open fenestration may be considered as a final surgical option for certain high-risk patients.