The cavotricuspid isthmus (CTI) is crucial in the ablation of typical atrial flutter (AFL), and consequently the CTI anatomy and/or its relation to resistant ablation cases have been widely described in human angiographic studies. Intracardiac echocardiography (ICE) has been shown to be a useful tool for determining detailed anatomical information. Thus, this technology may also allow the visualization of the anatomical characteristics of the CTI, providing an opportunity to further understand the anatomy. We conducted a study to compare the anatomy of the CTI between the patients with and without AFL and to characterize the anatomy of the CTI in the patients with AFL resistant to ablation. Twelve patients with typical AFL and 20 without AFL were enrolled in the study. Two-dimensional (2D) intracardiac echocardiography (ICE) was performed. The recordings were obtained with a 9F, 9-MHz ICE catheter from the right ventricular outflow tract to the inferior vena cava by pulling the catheter back 0.3 mm at a time under guidance with echocardiographic imaging in a respiration-gated manner. Three-dimensional (3D) reconstruction of the images of the CTI were made with a 3D reconstruction system. After the acquisition of the ICE, the CTI ablation was performed in the patients with AFL. The 2D and 3D images provided clear visualization of the tricuspid valve, coronary sinus ostium, fossa ovalis and Eustachian valve/ridge (EVR). The CTI was significantly longer in the patients with AFL than in those without AFL (median length 24.6 mm (range 17.0-39.1 mm) versus median length 20.6 mm (range 12.5-28.0 mm), respectively, P < 0.05). However, a deep recess due to a prominent EVR was observed in 9 of 12 (75%) patients with AFL and in 12 of 20 (60%) patients without AFL (N.S.). A deep recess and the relatively long CTI were related to aging in all the study patients, and that relationship was similar in a limited number of patients without AFL. In five patients with AFL resistant to ablation, a deep recess and prominent EVR were observed. The 2D and 3D ICE were useful for visualizing the complex anatomy of the CTI and identifying the anatomical characteristics of the CTIs refractory to ablation therapy. The anatomical changes observed in the CTI region may simply be the result of aging and may partially be involved in the development of AFL.