We report the case of a patient with heterotaxy syndrome including complex single ventricular morphology and interrupted IVC in association with twin conduction systems and a nodoventricular accessory pathway connection. The presence of 3 distinct QRS morphologies was inadvertently discovered during a hemodynamic catheterization study and prompted formal EP testing prior to hepatic venous inclusion into the Fontan circuit and loss of access to the atrial chamber for testing and therapy. This patient underscores the importance of close surveillance and high index of suspicion of arrhythmia mechanisms in patients with heterotaxy syndrome in conjunction with single ventricle morphology.