A 42-year-old man was referred to our hospital due to chest pain, diabetes mellitus, and sensorineural hearing loss. Transthoracic echocardiography revealed diffuse left ventricular hypokinesis. He was diagnosed with mitochondrial disease and a c.A3243G mutation was identified in his mitochondrial DNA. This case of mitochondrial cardiomyopathy demonstrated a low uptake of 123I-BMIPP, while the uptake of 99mTc-MIBI was preserved. In contrast, previous reports have noted the increased uptake of123I-BMIPP and the decreased uptake of 99mTc-MIBI. This is the first study to show this unique 99mTc-MIBI/123I-BMIPP mismatch pattern. We also discuss the relationships among the cardiac scintigraphy, cardiac magnetic resonance imaging, and histopathology findings.