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BACKGROUND: Many diverse pathogenic mitochondrial DNA (mtDNA) mutations have been described since 1988. The Melbourne Neuromuscular Research Institute (MNRI) has undertaken diagnostic detection of selected mtDNA mutations since 1990. MtDNA mutations screened have included point mutations associated with Leber's hereditary optic neuropathy (LHON; G3460A, G11778A and T14484C), mitochondrial encephalopathy lactic acidosis and stroke-like episodes (MELAS; A3243G), myoclonus epilepsy and ragged red fibres (MERRF; A8344G) and Leigh's syndrome/neuropathy ataxia retinitis pigmentosa (LS/NARP; T8993C/G). Samples have also been screened for deletions/ rearrangements associated with Kearns-Sayre syndrome (KSS) and chronic progressive external ophthalmoplegia (CPEO). AIMS: To present an audit of the MNRI mtDNA diagnostic service between 1990 and 2001, encompassing 1725 referred patients. METHODS: The detection techniques carried out included polymerase chain reaction amplification of mtDNA combined with restriction fragment length polymorphism analysis for mtDNA point mutation detection, supplemented with selected sequence analysis and Southern blots for the detection of deletions/ rearrangements. Tissues tested included blood, hair and skeletal muscle. RESULTS: Of the 1184 patients screened for MELAS A3243G, 6.17% were positive for the mutation, whereas for MERRF A8344G, 2.21% carried the mutation and for LS/NARP T8993C/G, 0.32% carried the mutation. The outcomes for the LHON mutations were G11778A, 6.60%, T14484C, 5.76% and G3460A, 0.29%. Of the patients referred for KSS and CPEO, 17.72% had deletions/rearrangements. CONCLUSIONS: Overall, the detection rate of mtDNA point mutations was low. The protean clinical features of mitochondrial disorders and the frequency of partial phenotypes lead to requests for tests in many patients with a relatively low likelihood of mtDNA mutations. An improved algorithm could involve mutation screening appropriate to the phenotype using sequencing of selected mtDNA regions in patients with a high likelihood of mtDNA disease. Features increasing the likelihood of mtDNA mutations include the following: (i) a typical phenotype, (ii) a maternal inheritance pattern and (iii) histochemical evidence of mitochondrial abnormality in the muscle biopsy. Efficient laboratory diagnosis of mtDNA disease involves good communication between the physician and laboratory scientists, coupled with screening of the appropriate tissue.