A 29-year-old white woman with typical angina pectoris presented diastolic dysfunction and was suggestive of isolated non-compaction of the ventricular myocardium (INCM) by echocardiography. Cardiac catheterization disclosed normal coronary arteries. Cardiovascular magnetic resonance (CMR) depicted prominent left ventricular INCM areas with non-compaction/compaction ratio of 3.7, and dipyridamole CMR demonstrated global perfusion defect at stress and normal perfusion at rest. Adenosine-induced vasodilation showed subnormal coronary velocity flow reserve in the right, left circumflex, and left anterior descending coronary arteries. The evidence of our case indicates that patients with INCM may present angina pectoris and, probably, relative chronic myocardial ischaemia related to an impaired microvascular function is responsible for this symptom as demonstrated invasively here. It is a possible mechanism for progressive myocardial dysfunction seen in these patients.