Hypertrophic cardiomyopathy is a complex disorder with significant heterogeneity in clinical characteristics and natural history. Traditionally, the diagnosis has been based on clinical assessment and echocardiography; however, persistent challenges in its noninvasive evaluation remain. Hence, improved diagnostic techniques could lead to better risk stratification of patients, which would potentially identify patients likely to benefit from effective therapies. Recent studies have demonstrated the increasing utility of cardiac magnetic resonance in the management of this disease. With the increasing utilization of genetics, cardiac magnetic resonance is likely to play an even more important role in discerning the subtle morphologic differences seen in such patients with similar genotypic profiles.