BACKGROUND Mitochondrial encephalomyopathies are heterogeneous diseases with common clinical features of muscle and/or the central nervous system. Although molecular and histological diagnoses have been established, imaging modalities for the functioning evaluation of these patients are still obscure. In this study, we tried to use 99mTc-HMPAO brain SPECT images to analyze various mitochondrial encephalomyopathies. METHODS We examined 99mTc-HMPAO Brain SPECT studies of 15 patients with various types of mitochondrial encephalomyopathy (3 Leber's hereditary optic neuropathy (LHON), 4 Kearns-Sayre syndrome (KSS), 4 mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes (MELAS), 3 myoclonic epilepsy and ragged-red fiber disease (MERRF), and 1 Leigh syndrome), diagnosed by molecular studies. RESULTS The results of our studies show obviously decreased radiotracer accumulation in the parieto-temporal regions after stroke-like episodes in patients with MELAS and MERRF: Relatively diminished brain perfusion in patients with KSS is noted, probably secondary to severe encephalomyopathy or subdural effusion. However, there seems to be no significant correlation between the clinical manifestations and the imaging findings in LHON and Leigh. CONCLUSIONS 99mTc-HMPAO Brain SPECT is useful in the diagnosing and assessment of the progress of MERRF, MELAS and KSS. However, its role in LHON and Leigh syndrome seems to be debatable.