The outcome of children born with cyanotic congenital heart disease has markedly improved over the years. Follow up is recommended for most post-operated cases as complications may occur over long term. One of the complications is the development of ventricular dysfunction, often seen after a successful Fontan surgery (or one of its modifications) for single ventricle. The aim of this study was to determine the prevalence of myocardial perfusion abnormalities in the ventricular myocardium of asymptomatic patients, older than 8 years of age, who had earlier undergone either a univentricular palliation (modified Fontan procedure) or a biventricular repair for tetralogy of Fallot, more than a year ago. All eligible patients underwent screening electrocardiogram (to rule out rhythm disturbance) and echocardiography. Patients with ventricular ejection fraction of more than 50 % by echocardiography were included. Enrolled patients were subjected to gated stress–rest myocardial perfusion imaging using Technitium-99m tetrofosmin single photon emission-computerized tomography (SPECT). Ventricular ejection fraction was also calculated from gated rest study. For the Fontan group, we also analyzed data to see if the morphology of the systemic ventricle would make a difference as far as myocardial perfusion was concerned. Twenty-six patients were enrolled (11 had undergone Fontan surgery and 15 had complete repair of tetralogy of Fallot). Seven of 11 patients in the Fontan group had myocardial perfusion defects (63.6 %) as against none in the repaired tetralogy of Fallot group (p < 0.001). The ejection fraction was within normal range in both the groups; it was statistically higher in the post tetralogy of Fallot repair group (p < 0.04). There were two subgroups in the post Fontan group depending on the morphology of systemic ventricle-left (4 patients) and non-left (7 patients). Higher number and larger size of perfusion defects were present in the non-left ventricular systemic ventricle morphology as compared with left ventricular morphology, but this difference did not reach statistical significance. Myocardial perfusion defects are common in patients who have undergone univentricular repair more than one year ago in contrast to patients who had a biventricular repair for tetralogy of Fallot. In the Fontan group, the morphology of the systemic ventricle was not predictive of prevalence of perfusion defect.