Histopathologic hallmarks of hypertrophic cardiomyopathy (HCM) include myocyte hypertrophy and disarray as well as interstitial and endocardial fibrosis. Published correlations between echocardiographic parameters and histopathologic findings are scarce. All patients aged <20 years (n = 45; 15 female patients; median age, 14 years) with obstructive HCM undergoing septal myectomy at the Mayo Clinic from 2003 to 2007 were identified. A retrospective review of echocardiographic data was performed, and these data were compared with the histologic findings from the myectomy specimens. Histopathologic analysis of myectomy specimens revealed significant myocyte hypertrophy (100%), myocyte disarray (98%), interstitial fibrosis (95%), and subendocardial fibrosis (97%). On multivariate regression analysis, there was a significant relationship between the degree of myocyte disarray and echocardiographic markers of left ventricular diastolic dysfunction. The results of this study suggest that myocyte disarray is a key factor responsible for diastolic dysfunction in pediatric patients with obstructive HCM. These findings provide novel insights into the mechanism of diastolic dysfunction in HCM that warrant further study.