Objectives. Cryoablation (CRYO) is an alternative to radiofrequency (RF) for catheter ablation of cavotricuspid isthmus (CTI)-dependent atrial flutter (AFL). We aimed to study whether different CTI morphologies had different impacts on procedural success for CRYO and RF. Design. This study randomized 153 patients with CTI-dependent AFL (median age 65 years; range 34–82) to RF or CRYO (78 CRYO; 75 RF). Biplane angiography (RAO 30° and LAO 60°) was done before the ablation procedure and isthmuses were classified as straight (n = 81), concave (n = 43) or pouch-like (n = 29). RF was performed with a 3.5-mm open-irrigated tip catheter and CRYO was performed with a 9 F, 8-mm tip catheter. The ablation endpoint was bidirectional block of CTI. Results. Acute procedural success was achieved in 70/75 patients in the RF group and in 72/78 patients in the CRYO group. With regard to CRYO or RF, acute procedural success rates were similar between the three isthmus types: straight: CRYO (92%) and RF (96%); concave: CRYO (92%) and RF (94%); and pouch-like: CRYO (94%) and RF (85%). There were no significant differences regarding success rate between the different morphologies in the CRYO or the RF group. The CTI was longer in patients with acute failure compared to the patients with acute success (38 ± 7 mm versus 33 ± 6 mm, p = 0.045). Conclusion. The CTI morphology did not influence the acute success rate for either the CRYO or the RF ablation of CTI-dependent AFL. A longer CTI was associated with a lower success rate regardless of energy source.