The purpose of this study was to report 18 cases of criss-cross heart and to evaluate the utility of magnetic resonance imaging (MRI) for the determination of atrioventricular segmental situs and atrioventricular alignment in patients with criss-cross heart. From August 1999 to March 2007, 18 consecutive patients with criss-cross heart were studied using a 1.5T MR scanner. Echocardiography and x-ray angiocardiography were performed in all patients and surgery was performed in 12 patients. MR examination resulted in the same diagnosis with x-ray angiocardiography in 94.4% of patients (17 of 18). The visceroatrial situs was solitus in 17 patients with normal left side heart position in 14 and dextrocardia in 3. The visceroatrial situs was inversus in 1 patient with dextrocardia. The atrioventricular connections were concordant in 17 patients and discordant in 1. In all patients, the right ventricle was located superiorly and the left ventricle inferiorly. Criss-cross heart is a rare malformation caused by abnormal rotation of ventricles in the embryo. Diagnosis of criss-cross heart is difficult and MRI was very helpful. MRI allowed clear visualization of the horizontal ventricular septum, the crossing inflow streams, atrioventricular segmental situs, atrioventricular alignment, and other malformations.