Objective: To observe the diagnostic accuracy of multi-detector CT (MDCT) in assessing myocardial function and myocardial fibrosis of hypertrophic cardiomyopathy (HCM) compared with cardiac MRI. Methods: Sixty consecutive patients confirmed of HCM clinically underwent cardiac CT and MRI. CT images were acquired in the arterial phase and the late phase. Cardiac MRI was performed with morphological and delay contrast-enhanced examinations. Left ventricular wall thickness, ejection fraction (EF), stroke volume (SV), left ventricle mass (LVM), cardiac output (CO), cardiac index (CI), left ventricular end-diastolic volume (EDV), left ventricular end-systolic volume (ESV), qualitative and quantitative diagnosis of lesion's delayed enhancement were compared between CT and MRI. Results: Sixty patients had 1020 myocardial segments. LV wall thickness measured with CT correlated with MRI results (r=0.895, P<0.001). Other cardiac function indexes, including SV, EF, LVM, EDV and ESV of CT correlated well with MRI. CT delayed enhancement in detecting myocardial fibrosis lesions had excellent correlation with MR delayed enhancement (r=0.98, P<0.01). Conclusion: Comprehensive cardiac CT can provide morphological and functional information of myocardium and coronary arteries.