The investigation of mtDNA disease can be relatively straightforward if a p
erson has a recognisable phenotype and if it is possible to identify a know
n pathogenic mtDNA mutation. The difficulties arise when no known mtDNA def
ect can be found, or when the clinical abnormalities are complex and not ea
sily matched to those of the more common mitochondrial disorders. We will d
escribe here the difficulties that can be encountered during the identifica
tion of pathogenic mtDNA mutations and the approaches that can be used to c
onfirm, or eliminate, a likely pathogenic role, in either single gene disea
ses or in multifactorial disorders.