Transseptal puncture is the most commonly used technique to perform electrophysiological procedures in the left atrium. This case report describes a pulmonary vein isolation in a patient with a paroxysmal atrial fibrillation, complicated by the presence of an oversized Amplatzer device (AGA Medical Corp., Golden Valley, MN). A retrograde approach using the magnetic navigation system (Niobe, Stereotaxis Inc., St Louis, USA) was performed, and showed to provide a feasible, safe and successful alternative for catheter ablation of cardiac arrhythmias in patients in whom the classic transseptal approach is impossible.