Objectives To assess the value of cardiac MRI in comparison to echocardiography in consecutive patients with previously diagnosed and new suspected hypertrophic cardiomyopathy (HCM). Methods All MRI studies of patients with HCM or suspected disease performed at our centre within a 10-year time period were evaluated. Initial diagnoses (echocardiography-based) and final (MRI-based) diagnoses were compared in subgroups, and the discrepancies were recorded. Results A total of 1006 subjects with HCM or suspected HCM were identified (61% males, 39% females; median age, 49.1 years; interquartile range, 34.9–60.4). In 12 (2.2%) out of 550 patients with known HCM, MRI indicated a diagnosis other than HCM, including but not limited to the subaortic membrane ( n  = 1, 8.3%) or mild left ventricular hypertrophy ( n  = 5, 41.7%). Among all patients with suspected HCM ( n  = 456), MRI diagnosis was different from HCM in 5.3% ( n  = 24) of patients. In an additional 20.4% of patients ( n  = 93), no significant hypertrophy was present. In total, among patients with suspected HCM, MRI led to clear HCM diagnosis in 204 (44.7%) patients. Among patients with a history of uncontrolled hypertension suspected of having HCM, MRI aided in identifying cardiomyopathy in 47.9% of patients. This subgroup contained the largest proportion of patients with an ambiguous diagnosis, namely, 29.6% compared with 13.8% in the remaining groups of patients with suspected HCM ( p  = 0.0001). Conclusions In a small but important group of patients with ultrasound-based HCM, cardiac MRI can diagnose previously unknown conditions and/or refute suspected cardiomyopathy. The diagnostic yield of MRI when compared to echocardiography in patients suspected of having HCM is 44.7%. Key Points • Out of 550 patients previously diagnosed with echocardiography but without magnetic resonance imaging (MRI) as having hypertrophic cardiomyopathy (HCM), we diagnosed a different disease in 12 (2.2%) patients using MRI. • Among patients with suspected HCM based on echocardiography, MRI led to clear HCM diagnosis in 44.7% of patients. • In patients with a history of uncontrolled hypertension suspected, based on an echocardiogram, of having HCM, MRI aided in identifying cardiomyopathy in 47.9% of patients. This subgroup contained the largest proportion of patients with an ambiguous diagnosis.