Impaired coronary flow velocity reserve and narrowing of intramyocardial small coronary arteries have been proposed as potential mechanisms for myocardial ischemia in hypertrophic cardiomyopathy (HCM). However, the relationship between them remains unclear. The purpose of this study was to evaluate the relation between coronary flow velocity reserve of left anterior descending coronary artery (LAD) and narrowing of intramyocardial small coronary arteries in patents with HCM. Methods Study population consisted of 14 patients with HCM without significant epicardial coronary artery stenosis by coronary angiography. Detection and localization of intramyocardial small coronary artery (ISCA) narrowing was determined by acceleration color Doppler flow signals within the ISCA. Narrowing of ISCA was calculated by the continuous equation; % area stenosis = [1- (peak velocity at proximal-acceleration site/peak velocity at acceleration site)] x 100. Coronary flow velocity reserve (CFVR), calculated as the ratio of hyperemic to basal peak diastolic LAD flow velocity induced by intravenous infusion of adenosine triphosphate (0.14 mg/kg/min), was examined in 14 patients with HCM and 9 normal subjects using transthoracic Doppler echocardiography. Results (1) Compared to normal subjects, CFVR was significantly lower in patients with HCM (3.6짹1.0 vs. 2.1짹1.1, p<0.005). (2) In patients with HCM, the velocity at the site of acceleration flow signal in the ISCA was significantly higher than that at the proximal site (112짹41 vs. 55짹14 cm/s, p<0.001), and the % area stenosis calculated by the continuity equation was 46짹18 % at the acceleration site. Furthermore, % area stenosis in the ISCA showed significant and good correlation with CFVR in the LAD (r=-0.817, p<0.05). Conclusion Impaired coronary flow velocity reserve of left anterior descending coronary artery in patients with hypertrophic cardiomyopathy would be related to the intramyocardial small coronary artery stenosis.