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The presence of septal hypertrophy in hypertrophic cardiomyopathy (HCM) is common. To date, there has been no accepted classification of septal morphology in HCM. Furthermore, the possible relationship between septal morphology and clinical features of HCM is undefined.Seventy-five consecutive adult patients with HCM were enrolled. Septal morphologies were retrospectively categorized into one of four patterns of hypertrophy based on transthoracic echocardiography. Left ventricular diastolic function by Doppler echocardiography and late gadolinium enhancement (LGE) by magnetic resonance imaging were assessed in all patients. Patients were followed for a mean of 45 ± 32 months. Catenoid septum was the most common morphologic subtype (46 of 75, 61%), followed by simple sigmoid (22 of 75, 29%), neutral (4 of 75, 5%), and apical (3 of 75, 4%). Inter-observer reproducibility of septal classifications was high (κ = 0.95). Patients with the catenoid subtype presented at a younger age, had worse diastolic function, and high rates of LGE. The presence of catenoid septal morphology was independently associated with LGE in multivariable logistic regression analysis. Implantable cardioverter-defibrillator implantation for prevention of sudden cardiac death occurred only in patients with this septal morphology.We propose a simple, reproducible classification system of patterns of septal hypertrophy in HCM. These patterns of hypertrophy are associated with significant differences in clinical, haemodynamic, and myocardial characteristics. Further studies are needed to evaluate the relationship between septal morphology and outcome or response to therapies in HCM.