A cohort of Malaysian patients with clinico-pathological diagnosis of three specifi c mitochondrial encephalomyopathy syndromes comprising of mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes (MELAS), myoclonus epilepsy with ragged-red fi bers (MERRF) and Leigh syndrome were studied to determine the frequency of their common mitochondrial DNA mutations. The ‘hot-spot’ point mutations for MELAS, MERRF and Leigh syndrome were screened. In the absence of common point mutations, screening of large-scale deletions as well as sequencing of tRNALeu and tRNALys genes were performed. Of 22 patients studied, nine m.3243A>G mutations, four m.8344A>G mutations, one m.8993T>G mutation and one deletion were identifi ed (65% detection rate). While the m.3243A>G mutation was closely associated with MELAS, the m.8344A>G was more heterogenous, being seen in one MERFF, two isolated mitochondrial myopathies and one Leigh syndrome patient. Screening for m.8993T>G in Leigh syndrome has a low yield as unsurprisingly Leigh syndrome has considerable genetic heterogeneity.