BACKGROUND There are several potential physiological differences between the atriopulmonary (AP) and the total cavopulmonary connection (TCPC) Fontan circulations. Studies suggest that the TCPC reduces energy loss due to turbulence and may have more dependence on respiratory movement for pulmonary blood flow. We compared cardiopulmonary physiology during rest and exercise in patients who had undergone the AP Fontan procedure with those who had undergone the TCPC Fontan procedure. RESULTS Forty-three children were studied more than 6 months after undergoing a Fontan procedure (23 AP and 20 TCPC); 106 healthy children were also studied as a control group. Measurements of effective pulmonary blood flow, stroke volume, arteriovenous oxygen difference, minute ventilation, heart rate, and oxygen and carbon dioxide consumption were made with an Innovision quadrupole mass spectrometer. Data from the control group allowed calculation of z scores for the Fontan groups matched for age, sex, pubertal stage, and body surface area. Maximal exercise performance was equal in the two Fontan groups, but it was below normal. However, adaptation to exercise was different in the Fontan groups. After 9 minutes of exercise, pulmonary blood flow rose less in the AP group than in the TCPC group (P < .01), and the stroke volume in the AP group also tended to be lower (P = .057) and their arteriovenous oxygen difference was significantly greater (P < .01). Although minute ventilation per unit of carbon dioxide production was similar in the Fontan groups at this level of exercise, children in the TCPC group breathed faster by approximately 10 breaths per minute (P < .005). CONCLUSIONS At submaximal exercise, children who had undergone the TCPC Fontan procedure had pulmonary hemodynamics superior to those of children who had undergone the AP procedure, largely because of respiratory adaptation that permitted blood to be "sucked" into the lungs. To achieve the same maximal exercise performance, children who had undergone the AP procedure had a superior metabolic adaptation to exercise stress.