BACKGROUND: The understanding of spontaneous scar-based reentrant atrial arrhythmia is limited. We aim to characterize the electrophysiologic and mapping features of spontaneous scar-based atrial flutter (AFL) and outcomes of catheter ablation. METHODS: Consecutive patients with a diagnosis of AFL who underwent catheter ablation from January 2012 to June 2015 were screened. Scars were detected in 12 patients and were included in this study. All had negative coronary angiography. These patients were divided into right AFL (seven patients) and left AFL groups (five patients) based on electrophysiologic mappings. RESULTS: Compared to patients with right AFL, the size of right atrium (RA) was smaller and left atrium (LA) was larger in the left AFL group. The proportion of the scar area was 11.1 ± 11.7 % in the RA AFL group and 7.8 ± 2.8 % in the LA AFL group. The difference was significant (P = 0.001). The acute success rates of ablation were 85.7% and 100%, respectively, in patients with right and left AFL (P = 0.304). During the follow-up, expansion of the scar area was noted in three patients with recurrent right AFL. No scar expansion was noted in one patient with recurrent left AFL. In addition, three patients with right AFL required permanent pacemaker implantation for sinus node dysfunction, and no one required pacemaker in patients with left AFL. CONCLUSIONS: Spontaneous scar could serve as substrate for AFL in RA or LA. Compared to left AFL, there was a higher rate of recurrence and pacemaker implantation in patients with right AFL.