BACKGROUND Right-side heart function is essentially externalized during extracardiac total cavopulmonary connection. The Fontan procedure has a certain impact on pulmonary hemoperfusion and may explain various postsurgical complications. In this study, alterations of pulmonary perfusion in patients undergoing the Fontan procedure were analyzed at the 5-year postoperative mark by radionuclide imaging and angiocardiography, and results of both methods were compared. METHODS For 43 post-Fontan patients, perfusion ratios of each lung segment were calculated based on radionuclide imaging data. The pulmonary vascular resistance and pulmonary artery index of each patient were also calculated from right angiocardiographic measurements. RESULTS The radionuclide count and advantage perfusion ratio of right lung at follow-up did not differ significantly from early postoperative values (t=0.38, p>0.05; t=1.12, p>0.05), and superior/inferior vena cava perfusion ratios were stable (t=0.88, p>0.05; t=0.74, p>0.05). The superior/inferior segment perfusion ratio of the whole lung declined significantly (t=2.54, p<0.05), while that of the dorsal lung segment rose significantly (t=2.16, p<0.05). Compared with early postoperative status, the pulmonary arterial index of patients at follow-up were significantly increased (t=2.41, p<0.05), while small pulmonary vascular resistances declined significantly (t=2.08, p<0.05; t=2.69, p<0.05), and arterial oxygen saturation levels were unaltered (t=1.12, p>0.05). The early angiographic and radionuclide perfusion studies of 5 patients did not match. CONCLUSIONS After the Fontan procedure, hypostatic redistribution of pulmonary blood flow is characteristic. The weak pulse of blood, in the absence of ventricular ejection, can promote pulmonary vascular changes, but at later (intermediate) follow-up, the decline in vascular resistance that results carries no benefit in terms of blood perfusion or oxygenation. Microcirculatory arteriovenous shunting is the likely cause. In this study of functional pulmonary hemoperfusion, radionuclide imaging was deemed superior to angiocardiography.