Background Since its introduction as a catheter navigation modality, the magnetic navigation system (MNS) has been used extensively for atrial fibrillation (AF) ablation. Nevertheless, the benefits of the system over manual technique remain unclear. The present study aims to compare the MNS to manual navigation with respect to clinical outcomes and procedural parameters. Subjects and Methods 120 consecutive patients undergoing catheter ablation for AF between March 2009 and April 2010 were enrolled in the study. Of these procedures, the first 72 were navigated by manual technique and the subsequent 48 by magnetic technique using the Niobe (Stereotaxis, Inc., Saint Louis, MO, USA) MNS. Procedures were evaluated in terms of acute success, mid-term success at 3-month follow-up, procedure time, and fluoroscopy time. The overall study population was divided into paroxysmal and persistent AF subgroups. Procedural success was defined as complete electrical isolation of the pulmonary vein antrum. Results For patients with paroxysmal AF, the MNS group was associated with significantly longer total procedure times (335 짹 48 vs. 292 짹 76 minutes, p = 0.006), shorter fluoroscopy times (98 짹 15 vs. 233 짹 60 minutes, p < 0.0001), and a lower rate of acute success compared to the manual group. For patients with persistent AF, the MNS group was associated with significantly shorter fluoroscopy times (95 짹 15 vs. 196 짹 53, p < 0.0001) compared to the manual group. The MNS and manual groups did not differ significantly in terms of total procedure times (314 짹 99 vs. 280 짹 54, p = 0.14) and acute success rates in the persistent AF population. The MNS and manual groups were not significantly different with respect to AF recurrence, atrial flutter/atrial tachycardia recurrence, or total arrhythmia recurrence in either the paroxysmal or persistent AF populations. While no complications were observed in the MNS group, several manual patients suffered cardiac tamponade or other complications. Conclusion This study demonstrates that the MNS is highly effective and safe when used for catheter ablation of AF. This assessment is particularly evident in the population of patients with persistent AF and slightly dilated left atria. KEY WORDS: Radiofrequency ablation; Magnetic navigation system; Atrial fibrillation