To assess the effect of a modified Fontan operation on systemic venous blood flow and the hepatic circulation, we compared 11 patients having an atriopulmonary connection and 35 with total cavopulmonary anastomosis. The Doppler echocardiographic study of the caval venous, hepatic venous and portal venous flow was performed so as to calculate the pulsatility ratio and the variation of flow with respiration. All patients had undergone cardiac catheterization. In addition, we included specific laboratory investigations to assess function of various organs. Significantly lower maximum velocities of flow at inspiration (0.31+/-0.12 m/sec vs 0.45+/-0.14 m/sec) and expiration (0.23+/-0.09 m/sec vs 0.32+/-0.11 m/sec), less pulsatility (0.43 vs 0.16) and a lower ratio of systolic to diastolic velocity (1.22 vs 1.85) were found in the patients having a cavopulmonary as compared to an atriopulmonary anastomosis. Peak velocities of hepatic venous flow during inspiration and expiration were significantly lower in those with a cavopulmonary anastomosis (p = 0.001 and p < 0.001, respectively). In these patients, forward flow was extremely dependent on respiration, with decrease or cessation of antegrade flow during expiration in 22 patients. The velocity of portal venous flow was also significantly lower in these patients, although the pulsatility ratio did not differ significantly between the groups (0.5+/-0.21 and 0.57+/-0.23, respectively). The ratio of inspiratory and expiratory velocities showed no significant difference between the groups, nor was there any correlation between the pulsatility ratio of the venous vessels or the ratio of peak flow velocities during expiration and the mean systemic venous/right atrial pressure on postoperative cardiac catheterization. Hypoproteinemia was found in 8 patients after total cavopulmonary anastomosis; 9 of 10 patients with protein C deficiency belonged to this group. The dependence of hepatic venous flow on respiration in the presence of a chronically elevated systemic venous pressure in patients after the total cavopulmonary anastomosis may influence hepatic function in the postoperative period.