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The presence of apical pouches in hypertrophic cardiomyopathy (HCM) may portend poor prognosis. We sought to study if the use cardiac magnetic resonance imaging (CMR) improves the detection of apical pouches in HCM compared to echocardiography. A retrospective review was performed of all consecutive HCM patients with an apical pouch identified by CMR at Mayo Clinic from May 2004 to Sept 2011. Clinical data was abstracted and CMR and echocardiographic images were analyzed. There were 56 consecutive HCM patients with an apical pouch identified by CMR. The predominant morphological type was apical in 41 (73.2 %), followed by sigmoid in 6 (10.7 %), reversed curve in 6 (10.7 %) and neutral in 3 (5.4 %). Obstructive physiology or systolic anterior motion of the mitral valve leaflet was evident in 23 (41.1 %). Late gadolinium enhancement was present in 47 (87.0 %) patients. Apical pouches were detected in only 18 (32.1 %) patients on echocardiography. Even when intravenous contrast was used (29/56 patients), in 16/29 (55.2 %) pouches were missed on echocardiography. Pouch length and neck dimensions in systole and diastole, measured on CMR, were larger among those patients in whom pouches were detected on echocardiography suggesting only larger pouches can be identified on echocardiography. In the largest CMR series to date of apical pouches in HCM, we show that while apical pouches are most commonly seen in apical HCM, they can be found in other phenotypic variants. CMR is better suited for the evaluation of apical pouches compared to echocardiography even with the use of intravenous contrast. CMR is likely a better tool for evaluating the cardiac apical structures including apical pouches when clinically indicated.