Background A novel magnetic guidance system has been developed that allows the operator to remotely navigate an electrophysiology mapping/ablation catheter to precise locations in the heart for treatment of tachyarrhythmias. To date, this new technology has not been directly compared with the conventional approach. Objective To compare the use of the magnetic guidance system to the conventional approach for ablation of atrioventricular nodal reentry tachycardia. Methods Between November 2002 and October 2004, 28 patients with atrioventricular nodal reentry tachycardia treated with the magnetic guidance system were retrospectively compared with 28 matched control patients. Results Patients treated using the magnetic guidance system had similar procedure durations and fluoroscopy times compared with the matched controls. The only statistically significant difference between the groups was a longer time between insertion of the ablation catheter and placement of the first radiofrequency lesion in the magnetic guidance system cohort (23.3 ± 12.0 vs. 10.5 ± 13.9, p=0.001), possibly due to the research protocol. However, there was a trend toward a shorter total time that radiofrequency energy was applied in the magnetic guidance system cohort (5.2 ± 4.5 vs. 8.0 ± 7.2, p=0.087). There were no major complications or recurrences after at least 3 months of follow-up among the patients treated with the magnetic guidance system. Conclusion The magnetic guidance system appears to have similar, and possibly improved, clinical efficacy compared with conventional catheter navigation for the treatment of atrioventricular nodal reentrant tachycardia.