Objective: Evaluate safety and efficacy of Magnetic Navigation System (MNS) in a large series of patients during long-term follow up. Background: MNS has the potential for improving safety and efficacy based on atraumatic catheter design and superior navigation capabilities. Methods: In this prospective registry, 1.266 consecutive patients underwent ablation. Patients were divided into two age- and sex-matched groups. Ablations were performed either using MNS (group MNS, 457) or conventional manual ablation (group MAN, 809). Following parameters were analyzed: acute success rate, fluoroscopy time, procedure time, complications (major: pericardial tamponade, permanent atrioventricular (AV) block, stroke, pulmonary embolism, major bleeding, death; minor: minor bleeding, temporary AV block). Recurrence rate was assessed during an average follow up of 24±14 months. Subgroup analysis was performed for the following groups: isthmus dependent and atypical atrial flutter, atrial tachycardia, AV nodal re-entrant tachycardia, circus movement tachycardia, atrial fibrillation and ventricular tachycardia (VT). Results: MNS was equally effective as MAN in acute success rate for overall groups (91,5% vs. 91,5%, p=ns). MNS was more successful for VTs (85,5% vs. 67,1%, p=0.006) and AVRT (96,3% vs. 88,4%, p=0.05). In the MNS group less fluoroscopy was used for AVNRT (12±7 vs. 27±19, p<0.001) and VT (26±19 vs. 48±29, p<0.001), however, longer fluoroscopy times were registered for AF (58±19 vs. 47±25, p<0.001). Procedure times for the overall group were longer in the MNS group (191±92 vs. 173±77 min, p=0.003). During follow up no differences in recurrence were observed between MNS and MAN for the overall population and the subgroups. MNS was associated with less major complications (1,1% vs. 3,7%, p=0.004). The total numbers of complications were lower in group MNS (5,0% vs. 9,8%, p=0.002). Conclusions: Our data suggest that the use of MNS improves safety without compromising efficiency of ablations. MNS is more effective than manual ablation for VTs and AVRTs.