BACKGROUND Atrial flutter (AFL) is common after cardiac surgery. However, the types of post-cardiac surgery AFL, its response to catheter-based radiofrequency ablation, and its relationship to atrial fibrillation (AF) are unknown. RESULTS We retrospectively studied all patients who underwent mapping and ablation for AFL after cardiac surgery from January 1990 to July 2004. One hundred randomly selected patients without prior cardiac surgery (PCS) who underwent mapping and ablation of AFL served as the control population. A total of 236 patients formed the study population (mean age 62 + 13 years, 22% female) and 100 patients formed the control population (mean age 60 + 13 years, 25% female). The majority of patients without PCS had cavo-tricuspid isthmus (CTI)-dependent AFL when compared to patients with PCS (93% vs 72%, respectively, P < 0.0001). In contrast, scar-related AFL was more common in patients with PCS as compared to patients without PCS (22% vs 3%, P < 0.0001). Predictors of scar related AFL in multivariable regression analysis included PCS and left-sided AFL. Acute success rates and complications were similar between the groups. When compared to patients with AFL ablation without PCS, those that had AFL after PCS had higher rates of recurrence of both AFL (1% vs 12%, P < 0.0001; mean time to recurrence 1.85 years) and AF (16% vs 28%, P = 0.02; mean time to recurrence 2.67 years). CONCLUSIONS Despite ablation of AFL, patients with PCS have a higher rate of AFL and AF when compared to patients without PCS who underwent ablation of atrial flutter during long-term follow-up.