Energy inefficiencies lead to Fontan procedure failures. Our purpose was to quantify energy inefficiencies of various Fontan procedures using flow analysis.The study included 12 patients with Fontan operations; 7 with classic trans-atrial flow and five extra-cardiac Fontans. Flow analysis was used to determine the systolic and diastolic flow in the superior vena cava and inferior venous circulations (IVC, right atrium or conduit). Retrograde flow fractions were calculated. Inferior venous flow analysis was obtained in 12 patients and superior vena cava in 9 patients.A seesaw pattern (augmented inferior venous flow during diastole and augmented superior vena cava flow in systole) was present in five of seven patients with trans-atrial Fontan procedures, but no patient with an extra-cardiac Fontan procedure. Significant retrograde flow occurred in the superior vena cava in three children with trans-atrial Fontan procedures (retrograde flow fractions of 15-22%). Inferior venous flow occurred predominantly during diastole in five of seven children with trans-atrial Fontan procedures. Retrograde flow occurred in all seven children with the retrograde flow fractions ranging from 9 to 37% (mean 25%). Extracardiac Fontan flow was characterized by continuous balanced flow during systole and diastole. The association of the seesaw pattern with trans-atrial Fontan procedures was statistically significant (p = 0.028).Classic trans-atrial Fontan procedures are characterized by energy inefficiency creating a seesaw flow pattern of forward and reverse flow. Extra-cardiac Fontan procedures are more energy efficient. Magnetic resonance imaging is useful in detecting flow inefficiencies in patients palliated by the Fontan procedure.