Our aim was to compare the frequency and distribution of late gadolinium enhancement (LGE) on contrast MRI between hypertrophic cardiomyopathy (HCM) patients with apical hypertrophic cardiomyopathy (APH) and those with asymmetrical septal hypertrophy (ASH). We studied 66 patients with HCM (50 men and 16 women; average age: 58.8 ± 29.8 years) who had undergone MRI. All the MRI examinations were performed using a 1.5 T system. LGE images were acquired using the inversion recovery segmented spoiled-gradient echo and phase-sensitive inversion recovery methods. We evaluated 17 segments of the left ventricle as defined by the American Heart Association criteria for LGE determination. LGE was detected at the junction of the right ventricle and the interventricular septum in 25 (73.5%) of the 34 HCM patients with ASH and in the apex of the heart in 13 (40.6%) of the 32 patients with APH. LGE-positive areas were more widely distributed in the case of the ASH group than in the case of the APH group. The distribution of LGE was clearly different between the two groups (Fisher’s exact probability test, P = 0.0068). The number of LGE-positive cases and LGE-positive segments were significantly higher in the ASH group than in the APH group and there was a significant difference in the distribution of the LGE-positive areas between the two groups. LGE was mainly detected in the hypertrophied areas of the myocardium.