Common atrium (CA), also called three-chambered heart, is one of the rare congenital anomalies, defined by a complete absence of the atrial septum, eventually associated with malformation of the atrioventricular (AV) valves. We report the case of a 57-year-old woman with CA complicated with Eisenmenger syndrome and inferior vena cava interruption, who suffered from symptomatic persistent atrial fibrillation (AF). She underwent an initial successful pulmonary vein isolation procedure. A repeat procedure for perivalvular atrial flutter was complicated with inadvertent complete AV block, due to unusual AV node location in this challenging anatomy.