This study evaluated the prevalence, anatomical pattern, and prognostic implications of an intramural course of the coronary arteries in patients with hypertrophic cardiomyopathy (HC). The study population consisted of 92 patients with HC and 100 patients without HC. The presence of an intramural course of the coronary arteries was evaluated by coronary computed tomography angiography (CTA), and its length and depth were measured. During follow-up, the occurrence of unstable angina requiring hospitalization, myocardial infarction, and all-cause mortality was evaluated. An intramural course of the coronary arteries was more common in patients with HC than patients without HC (62% vs 25%, p <0.001). In the patients with an intramural coronary artery course, those with HC had a longer course (29.1 ± 15.3 mm vs 23.0 ± 13.0 mm; p = 0.037) with deeper penetration into the left ventricular myocardium (2.8 ± 1.2 mm vs 2.1 ± 0.8 mm; p = 0.007) and more involvement of multiple coronary arteries (38% vs 4%; p <0.001). During follow-up (mean 5.5 ± 3.5 years), cardiac events occurred in 17 of 57 patients (29.8%) with an intramural course and 11 of 35 (31.4%) without an intramural course (p = 0.87). On Kaplan-Meier survival analysis, there was no difference in cumulative event rate between HC patients with or without an intramural course (p = 0.89, log rank test). In conclusion, patients with HC have a high rate of an intramural course of the coronary arteries on CTA. The number of involved arteries and the length and depth of the intramural course differ between patients with and without HC, but apparently have no association with worse clinical outcomes.