Coronary artery obstruction is the main late complication of the so-called arterial switch operation designed to repair transpositions of the great arteries in newborn infants by switching the great vessels and transferring the coronary ostia onto the posterior vessel. Our aim was to study the links between myocardial perfusion and coronary artery anatomy after the arterial switch operation. Forty-five patients (5.863 years) underwent a 201Tl myocardial SPECT and a selective coronary artery angiography. The latter was normal in 20 children: 13 had also a normal myocardial scan but 7 had myocardial perfusion defects including 2 with angina who had a very low coronary reserve at positron emission tomography. Twenty-five patients had severe coronary artery lesions: 5 with a normal myocardial scan and 20 with perfusion defects. Twelve out of these 20 underwent surgical revascularization and the SPECT images went back to normal in all within 6 months after surgery. Specificity and sensitivity of myocardial SPECT in detecting coronary artery lesions were 78% and 69% whereas positive and negative predictive values were 74 and 73%. We conclude that myocardial SPECT imaging is not the right way to detect late post arterial switch coronary artery lesions. It is helpful in decision making as to submit these children to surgical revascularization and in assessing its postoperative effectiveness.