Contrast enhanced magnetic resonance imaging (CeMRI) reliably identifies myocardial fibrosis in patients with hypertrophic cardiomyopathy (HCM). However, many patients have contraindications to ceMRI. Previous studies have shown that contrast enhanced multi-detector computed tomography (ceMDCT) can visualize focal scars following myocardial infarction in experimental animals and patients. The purpose of this manuscript is to assess the ability of ceMDCT to detect focal myocardial scars in patients with HCM. Twelve HCM patients underwent ceMRI and ceMDCT. Fibrotic areas of myocardium were defined as focal or diffuse areas of fibrosis. The mean signal intensity in ceMRI and attenuation values in ceMDCT of the fibrotic regions, normal myocardium and left ventricle blood pool contrast were measured using qualitative and quantitative analysis. Focal scar mass was calculated using both techniques. Focal scars were detected in 9 patients and diffuse fibrosis was visualized in all patients by ceMRI. Differences between normalized SI of normal myocardium and focal scars, normal and diffuse areas of fibrosis, and diffuse fibrosis and focal scars were significant for both ceMRI and ceMDCT (p < 0.05). Diffuse fibrosis was poorly visualized by ceMDCT but was detectable using quantitative measurements. CeMDCT has potential to detect focal myocardial scars in patients with HCM who have contraindications to ceMRI study. However, ceMDCT does not enable adequate visualization of diffuse myocardial fibrosis, and thus is less well suited than ceMRI for assessment of total burden of fibrosis. This limitation may be overcome using quantitative methodology.