To explore the changes of pulmonary perfusion over 5 years in patients who underwent extracardiac total cavopulmonary connection. Forty-three patients who had undergone extracardiac total cavopulmonary connection were examined with pulmonary perfusion 1 month and 5 years following the operation. 99mTc-MAA was used for perfusion imaging; pulmonary perfusion value and blood distribution were measured and calculated. Vena cava pressure and arterial oxygenation were measured using the right cardiac catheter, and the pulmonary arteriole resistance was calculated. The status of the conduit connection was assessed by computed tomography three-dimensional reconstruction. Radionuclide counts of the follow-up group were similar to those of the early postoperative group, and the ratios of right to left pulmonary perfusion and inferior vena cava perfusion were not changed. However, the ratio of the whole pulmonary superior to inferior segment was remarkably reduced (t=2.54, P<0.05), with a significantly higher perfusion rate in the posterior segment of the lower lobe (t=2.16, P<0.05). The pulmonary arteriole resistance of the follow-up group was reduced significantly (t=2.08, P<0.05). The vena cava pressure was also reduced (t=2.69, P<0.05), but oxygenation was not significantly changed. Five patients showed a mismatch between pulmonary angiography and radionuclide scintigraphy soon after the operation. The pulmonary angiography showed that the anastomosis was patent, and both lungs were demonstrated. However, the radionuclide scintigraphy only demonstrated the unilateral lung soon after the operation, and both lungs were demonstrated during follow-up. Radionuclide scintigraphy is superior to the pulmonary angiography in the study of functional pulmonary perfusion. Fontan circulation may lead to gravity-dependent blood redistribution, and its weak pulsation can promote pulmonary vascular development. However, the reduced pulmonary arterial resistance at mid-term follow-up may not lead to an increased amount of pulmonary perfusion or oxygen supply, which is probably because of the massive opening of the arteriovenous shunt and increased futile circulation.