Objectives To evaluate the diagnostic performance of computed tomography (CT) in patients with hypertrophic cardiomyopathy (HCM) and suspected coexistent coronary artery diseases (CADs). Methods Sixty patients were enrolled in this study. Cardiac CT examination included CT coronary angiography (CTCA) and delayed enhancement CT. CT performance in evaluation of the coronary artery was assessed and compared with that of catheter-based coronary angiography (CA). The left ventricle (LV) wall thickness, functional indices and myocardial delayed enhancement (MDE) were measured via cardiac magnetic resonance (CMR) and CT images. Results Compared with catheter-based CA, CTCA produced a 100 % (24/24) sensitivity, a 94.4 % (34/36) specificity, a 92.3 % (24/26) positive predictive value and a 100 % (34/34) negative predictive value. CT-measured LV wall thickness and functional indices were correlated with those measured via CMR (P<0.01), though the CT-measured values were smaller than the CMR-measured values. Bland-Altman analysis showed the volume of the focal MDE determined via CT was slightly smaller than that determined using CMR (mean difference: 0.3 cm(3)). Conclusions For patients with HCM and suspected coexistent CAD, this comprehensive cardiac CT protocol can be helpful in ruling out coronary stenosis and can provide information regarding morphology, function and tissue characterization of the LV myocardium.