Background: Atypical atrial flutter (AFL) can be challenging to ablate, especially when involving dual-loop re-entry. We sought to assess the electroanatomical characteristics of single- and dual-loop AFLs in patients undergoing catheter ablation. Methods: We analyzed 25 non-cavotricuspid isthmus-dependent macro-re-entrant AFL in 19 consecutive patients. Three-dimensional high-density activation mapping was performed, and active re-entry loops were confirmed by entrainment mapping. Results: Of 25 AFLs (24 left, 1 right atrial), 13 (52%) exhibited dual-loop re-entry. The most common circuits included, in 6/13 (46% of dual loops), a perimitral re-entry with a second loop around the right/left pulmonary veins (PV) and, in 6/13 (46%), involved a right PV ostium with a second loop around either a functional conduction block or another PV. Ablation at the common isthmus of dual-loop AFLs and at the critical isthmus of single-loop AFLs terminated the arrhythmia more frequently than ablation at a secondary isthmus of dual-loop AFLs (5/6 (83%) and 8/11 (73%) versus 1/8 (13%), respectively, p = 0.013). Conclusions: More than half of AFLs exhibited a dual-loop re-entrant mechanism. Most critical isthmuses were found at the mitral isthmus, the left atrial roof or right PV ostia. Ablation targeting the common isthmus resulted in a higher termination rate.