Aims: We aimed to evaluate the safety and long-term efficacy of the magnetic navigation system (MNS) in a large number of patients. The MNS has the potential for improving safety and efficacy based on atraumatic catheter design and superior navigation capabilities. Methods and results: In this study, 610 consecutive patients underwent ablation. Patients were divided into two age-and sex-matched groups. Ablations were performed either using MNS (group MNS, 292) or conventional manual ablation [group manual navigation (MAN), 318]. The following parameters were analysed: acute success rate, fluoroscopy time, procedure time, complications [major: pericardial tamponade, permanent atrioventricular (AV) block, major bleeding, and death; minor: minor bleeding and temporary AV block]. Recurrence rate was assessed during follow-up (15 +/- 9.5 months). Subgroup analysis was performed for the following groups: atrial fibrillation, isthmus dependent and atypical atrial flutter, atrial tachycardia, AV nodal re-entrant tachycardia, circus movement tachycardia, and ventricular tachycardia (VT). Magnetic navigation system was associated with less major complications (0.34 vs. 3.2%, P = 0.01). The total numbers of complications were lower in group MNS (4.5 vs. 10%, P = 0.005). Magnetic navigation system was equally effective as MAN in acute success rate for overall groups (92 vs. 94%, P = ns). Magnetic navigation system was more successful for VTs (93 vs. 72%, P < 0.05). Less fluoroscopy was used in group MNS (30 +/- 20 vs. 35 +/- 25 min, P < 0.01). There were no differences in procedure times and recurrence rates for the overall groups (168 +/- 67 vs. 159 +/- 75 min, P = ns; 14 vs. 11%, P = ns; respectively). Conclusions: Our data suggest that the use of MNS improves safety without compromising efficiency of ablations. Magnetic navigation system is more effective than manual ablation for VTs.