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Background: The automated NavX Ensite Precision latency-map (LM) algorithm aims to identify atrial tachycardia (AT) mechanisms. However, data on a direct comparison of this algorithm with conventional mapping are scarce. Methods: Patients scheduled for AT ablation were randomized to mapping with the LM- algorithm (LM group) or to conventional mapping (conventional only group: ConvO), using entrainment and local activation mapping techniques. Several outcomes were exploratively analyzed. Primary endpoint was intraprocedural AT Termination. If AT termination with only automated 3D-Mapping failed, additional conventional methods were applied (conversion). Results: A total of 63 patients (mean 67 years, 34 % female) were enrolled. In the LM group (n = 31), the correct AT mechanism was identified in 14 patients (45 %) using the algorithm alone compared to 30 patients (94 %) with conventional methods. Time to termination of the first AT was not different between groups (LM group 34 ± 20 vs. ConvO 43.1 ± 28.3 min; p = 0.2). However, when AT termination did not occur with LM algorithm, time to termination prolonged significantly (65 ± 35 min; p = 0.01). After applying conventional methods (conversion), procedural termination rates did not differ between LM group (90 %) vs. ConvO (94 %) (p = 0.3). During a follow-up time of 20 ± 9 months, no differences were observed in clinical outcomes. Conclusion: In this small prospective, randomized study, the use of the LM algorithm alone may lead to AT termination, but less accurate than conventional methods.