AIMS Catheter ablation of isthmus-dependent atrial flutter is technically demanding in some patients and extremely simple in others. The intervention targets a defined anatomical structure, the so-called cavotricuspid isthmus (CTI). We sought to characterize CTI anatomy in vivo in patients with difficult and simple catheter ablation of atrial flutter. METHODS AND RESULTS Twenty-six patients were studied. Seven patients with difficult (n = 6) or extremely simple (n = 1) CTI ablation procedures were retrospectively selected from our catheter ablation database. Thereafter, we prospectively studied 19 patients undergoing CTI ablation in our department. We visualized CTI anatomy by ECG- and respiration-gated free precession 1.5 T cardiac magnetic resonance imaging (MRI). Magnetic resonance imaging was analysed for systolic and diastolic CTI length, the angle between the vena cava inferior and CTI, and pouch-like recesses. These parameters were compared between patients with difficult and simple procedures, split by the median number of energy applications. Patients with difficult procedures had a longer diastolic CTI length (diastolic isthmus length 20.3 +/- 1.8 mm) than those with simple procedures (diastolic isthmus length 16.6 +/- 1.7 mm, all data as mean +/- SEM, P <0.05). Cavotricuspid isthmus angulation with respect to inferior vena cava was closer to 90 degrees in patients with difficult procedures (deviation from 90 degrees: 15 +/- 2 degrees) than those with simple procedures (deviation 23 +/- 4 degrees, P <0.05). Systolic CTI length was not different between groups (32 +/- 2 mm in both groups, P > 0.2). CONCLUSION Longer diastolic, but not systolic, CTI length and a rectangular angle between CTI and inferior vena cava render CTI catheter ablation difficult. Visualization of isthmus anatomy may help to guide difficult CTI ablation procedures.