Atrial tachycardias are relatively common in patients with congenital heart disease. However, complex anomalies involving the heart and the great vessels might compromise the results of the ablation procedure. This report describes a clinical application of the new Cartosound™ module as an adjunctive technology to understand the mechanism of the arrhythmia and to guide successfully the ablation in a complex anatomy. Isthmus-dependent atrial flutter was diagnosed in a patient with complete situs inversus and interruption of the inferior vena cava with azygos continuation. Under these unusual circumstances, Cartosound facilitates interventional navigation within the right atrium and its adjacent structures and minimizes radiation exposure.