BACKGROUND Transposition of the Great Arteries (TGA) is a cyanotic congenital heart defect characterized by an incorrect origin of the great arteries from the cardiac ventricles. Currently, the first-line surgical correction for TGA is the "arterial switch" procedure, which restores the correct positioning of the great arteries. This approach has replaced earlier techniques like the atrial switch procedures of Mustard or Senning. These procedures aimed to restore serial circulation by creating intra-atrial baffles that redirected pulmonary venous return to the systemic (sub-aortic) ventricle and systemic venous return to the sub-pulmonary ventricle. The downside of this correction was the presence of a morphologically right ventricle in the sub-systemic position, which over time could develop systolic dysfunction and subsequent heart failure. CASE DESCRIPTION A 33-year-old woman, treated in neonatal age with Mustard procedure due to TGA, presented to the Emergency Department with sudden onset of right-sided facial, brachial and crural hypoesthesia upon waking. The stroke protocol identified an ischemic area in the left posterolateral thalamo-capsular region, and timely fibrinolytic therapy was administered, resulting in complete remission of the symptoms. The patient was subsequently admitted to our unit for etiological clarification. Examinations, including carotid ultrasound, glucose and metabolic profile, coagulation studies, thrombophilia screening, and autoimmune testing, were all negative. Neither Holter ECG nor telemetry detected atrial flutter or fibrillation. Thoracic/cardiac CT with contrast confirmed the known cardiac anatomy and showed no baffle obstruction. Given the negative findings, a paradoxical embolism via an intracardiac shunt was considered. Transthoracic echocardiography with agitated saline revealed rapid opacification of the systemic ventricle, indicating an intracardiac shunt at the atrial baffle level. Transcranial Doppler confirmed significant microbubble passage into the cerebral circulation. Anticoagulation therapy was started, and at six months follow-up, the patient remains asymptomatic. CONCLUSIONS The presence of a leak at the atrial baffle is an uncommon condition that should be suspected in patients with Mustard procedure and cryptogenic stroke.