Congenitally corrected transposition of great arteries (ccTGA) consists of both atrioventricular and ventriculo-arterial discordance. In patients with ccTGA, the pulmonary artery arises from the left ventricle, whereas the aorta arises from the right ventricle. The burden of the systemic blood pressure on the right ventricle involves an increased risk of coronary artery disease (CAD) and, as a long-term consequence, myocardial hypertrophy and gradual failure. This report describes the case of an adult patient affected by ccTGA who was referred for an episode of atypical chest pain while at rest. First-line diagnostic examinations were inconclusive. Myocardial perfusion single-photon emission tomography (SPET) was performed to exclude CAD, but the congenital abnormalities of the patient’s heart made interpretation of the images particularly difficult. A perfusion positron emission tomography–computed tomography (PET-CT) scan with ¹³N-ammonia then was suggested, which unmasked an unexpected artifact. The case report demonstrates that hybrid imaging techniques such as SPET-CT and PET-CT should be used systematically when CAD is suspected for patients with abnormal anatomy of the heart, including ccTGA.