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Brady-arrhythmias in patients undergone atrial switch procedures (Mustard or Senning procedure) for complete transposition of the great arteries (TGA) are common and often require implantation of permanent pacemakers. It has been shown that in patients with palliated congenital cardiac defects with residual intra-cardiac shunts, permanent pacemaker implantation is associated with an increased risk of thrombo-embolism. Patients with TGA and concomitant baffle leaks may have an even further increased thrombo-embolic risk, given that the leaks can provide the conduit for venous to systemic thrombo-embolism. In order to decrease this risk, all TGA patients who require pacemaker implantation typically undergo a thorough pre-procedural evaluation to assess for the presence of a baffle leak. Traditional imaging modalities, however, are often limited in their ability to detect and/or properly locate small baffle leaks. We report a case of a patient with TGA and a baffle leak that was both identified and percutaneously closed with the assistance of real-time 3D transoesophageal echocardiography.