Introduction: The endpoint of catheter ablation at complex fractionated atrial electrograms (CFAE) has been not elucidated yet. Furthermore, incomplete ablation of CFAE may have a potential to develop atrial tachycardia (AT), resulting in increasing recurrence after catheter ablation of atrial fibrillation (AF). We soughted to compare the efficacy of linear ablation extending the clusters of CFAE and focal ablation at the individual CFAE sites. Methods: A total of 132 patients (55.5짹10.0 years old, 85.6% male) with persistent AF in whom AF sustained after circumferential pulmonary vein ablation with electrical isolation using NavX 3D system were randomized to perform either focal ablation (focal-group, n=66) or linear ablation (linear-group, n=66) at CFAE. Primary endpoint was freedom from AF/AT more than 3 months after first ablation. This study is registered with Clinicaltrials.gov number NCT01088126. Results: Rate of sinus conversion and organization into AT during the CFAE ablation were more often observed in linear-group compared with focal-group, however, there was no statistical significance (63.6% vs. 51.5%, p=0.218; 66.7% vs. 63.6%, p=0.855). The rate of acute termination of AF was similar between two groups (81.8% in focal-group vs. 83.3% in linear-group, p=0.819). The incidence of early recurrence of AT was higher in linear-group than in focal-group (39.4% vs. 16.7%, p=0.006). During the mean 17.5짹7.4 months, Kaplan-Meier analysis showed that there was no significant difference in the freedom from recurrence of AF/AT between focal-group and linear-group (69.7% vs. 60.6%, p=0.188 by long-rank). Complications related to the procedure occurred in 8 patients (focal-group, 7 cardiac tamponade; linear-group, 1 femoral artery injury). Conclusion: Compared with focal ablation at the individual CFAE sites, linear ablation extending the clusters of CFAE resulted in higher incidence of early recurrence of AT, but has shown similar efficacy in freedom from AF/AT during the follow-up in patients with persistent AF.