Blood capillary abnormalities accompanied by intramural small arterial lesions were reported in patients with microvascular angina (MVA), hypertrophic cardiomyopathy (HCM), and dilated cardiomyopathy (DCM). We compared the ultrastructural changes of blood capillaries in myocardial biopsy samples from MVA, HCM, and DCM patients using electron microscopy and ultrastructural morphometry. Ten cross-sectioned views were selected from each patient at random, and the degree of cytoplasmic swelling of the endothelial cells was measured (transverse area of endothelial cell cytoplasm (E)/transverse area of the blood capillary (C)). The thickness of the basal lamina was also assessed (transverse area of basal lamina (BL)/C). The average value of the E/C ratio was in the order of control group < HCM < MVA < DCM, with significant differences among the groups (p < 0.001). The average value of the BL/C ratio was in the order of control group < MVA < HCM < DCM, with significant differences (p < 0.001) among the groups except between the HCM and DCM groups. In conclusion, swelling of the endothelial cells as well as luminal stenosis of small arteries and arterioles may be related to disturbed microcirculation in these patients.