Non-invasive cardiac imaging plays a central role in the diagnosis and management of patients with hypertrophic cardiomyopathy. Transthoracic echocardiography is the imaging technique of first choice to evaluate wall thickness, left ventricular systolic and diastolic function, presence of left ventricular outflow tract obstruction, and abnormal mitral anatomy, whereas cardiac magnetic resonance provides additional information on tissue characterization (replacement fibrosis) using late gadolinium enhancement. Nuclear imaging techniques permit also the assessment of left ventricular systolic and diastolic function in patients with hypertrophic cardiomyopathy but are more frequently used to evaluate myocardial ischemia (particularly assessment of microvascular dysfunction using positron emission tomography) and abnormal sympathetic myocardial innervation. This review article provides an overview of the use of nuclear imaging techniques to refine the phenotyping and risk stratification of patients with hypertrophic cardiomyopathy with particular focus on prediction of progression to overt heart failure, detection of myocardial ischemia, and evaluation of the arrhythmogenic substrate and risk of sudden cardiac death.