We describe a 12-year-old male with isolated noncompaction of the myocardium and associated abnormal calcification in the basal interventricular septum, and we present a review of the literature. The patient has been healthy and free of symptoms. The electrocardiogram showed abnormal Q waves in III, V1, V2, and ST elevation in V1–V3. Exercise testing demonstrated ST depression in V4 and V5. Myocardial scintigraphic examination showed a regional reduction in iodine-1,2,3-beta-methyl-iodophenylpentadecanoic acid uptake in the basal interventricular septum. Since coronary angiography demonstrated normal coronary vessels and the trabeculations were not prominent in this region, we hypothesize that coronary microcirculatory dysfunction may cause subendocardial infarction associated with calcification in the same area.