Hypertrophic cardiomyopathy (HCM) is characterized by extreme clinical heterogeneity, ranging from sudden cardiac death to long-term disease progression and heart failure-related complications. Myocardial ischemia, occurring at the microvascular level, is a major determinant of clinical expression and outcome. Accordingly, the severity of this microvascular dysfunction has been shown to represent an early and powerful predictor of unfavorable outcome in HCM. The assessment of microvascular function in vivo is technically challenging, although critical to a truly comprehensive evaluation and risk stratification of HCM patients. Available technologies include positron emission tomography and cardiac magnetic resonance (CMR). Studies of regional myocardial blood flow using positron emission tomography have demonstrated that the vasodilator response to dipyridamole is impaired in most HCM patients, not only in the hypertrophied ventricular septum but also in the less hypertrophied or non-thickened left ventricular free wall. CMR also allows measurement of myocardial flow, although the technique is currently time-consuming and largely limited to research situations. CMR provides further insight into the effects of ischemia in HCM patients, by visualizing the distribution and extent of fibrosis at the intramyocardial level. Late gadolinium enhancement (LGE) is a potential predictor of risk in HCM patients, and is believed to largely reflect replacement fibrosis resulting from recurrent microvascular ischemia. LGE is associated with increased prevalence of ventricular arrhythmias, and associated with microvascular dysfunction. The present review is to provide a concise overview for the available evidence of microvascular ischemia and its consequences in HCM.