BACKGROUND The purpose of this report is to outline technical maneuvers dictated by anomalies of systemic and/or pulmonary venous connection in the performance of the Fontan procedure. RESULTS Between 1975 and 1990, 104 patients (60 male, 44 female) with anomalies of systemic and/or pulmonary venous connection underwent a modified Fontan procedure at the Mayo Clinic. Mean age was 9.7 +/- 5.7 years. Isolated anomalies of the systemic venous connection were identified in 46 patients, isolated anomalous pulmonary venous connections in 4, and a combination of the two in 54. Previous palliative operations had been performed in 93 patients. Surgical repair was accomplished by atrial septation or placement of an intra-atrial conduit combined with cavopulmonary anastomosis if required. Survival by Kaplan-Meier, including operative mortality, was 55.7% at 10.3 years, not significantly different from the overall survival of the Fontan population. By the proportional hazards general linear model procedure, insufficiency of the systemic atrioventricular valve, preoperative mean pulmonary pressure greater than 15 mm Hg, and pulmonary artery resistance index greater than 4 U.m2 were associated with higher mortality. Five patients required reoperation for pulmonary venous obstruction (1 patient), revision of the atrial baffle (1 patient), revision of the intra-atrial conduit (2 patients), and replacement of the systemic atrioventricular valve (1 patient). CONCLUSIONS We conclude that the modified Fontan operation can be successfully performed in this subset of patients, with long-term results comparable to those obtained in patients with normal systemic and pulmonary venous connection.