Aim To determine whether electron-beam CT (EBCT) is useful as a noninvasive coronary artery calcification screening examination for differentiating diagnosis of hypertrophic cardiomyopathy (HCM). Methods Ninety and nine consecutive patients with HCM from 33 to 71 years old (48.6±12.7 years), were reviewed to find out clinical characteristics and implication of coronary artery calcification detected with EBCT scanning when simultaneously compared with 102 coronary heart diseases (CHD) patients, 30 to 78 years old (56.2±10.9 years). Results Of the 99 HCM patients, 31 (32.3%) had detectable coronary calcification, and calcium score was 21.1±4.9. There was a significant difference between HCM group and CHD group, which were 66.7%(68/102) and 203.2±34.9, respectively (p<0.01). The prevalence of coronary calcification and calcium score had a increase as age went up in HCM patients, but still in the range scores in normal chinese. The outcome was the same after age and gender adjustment. Conclusion EBCT is helpful to distinguish HCM patients from suspected CHD patients or associated CHD as a noninvasive imaging technique.