Mitochondrial encephalomyopathies are a heterogenous group of disorders with various biochemical defects of the respiratory chain (RC). Due to the considerable phenotypic diversity of the RC encephalomyopathies, they are included in the differential diagnosis of many cases of multisystem disease. Aside from clinical evaluation and family history, diagnosis can be supported by many other sources. The complexity of diagnostic information can make it difficult for the clinician to establish the level of certainty at which a RC cytopathy is diagnosed in atypical cases. We review the parameters (clinical, pathological, biochemical and molecular) which are used to aid diagnosis of RC encephalomyopathy and identify levels of abnormality in each that strongly or less strongly support the diagnosis. A system is developed that allows classification of the diagnosis in possible, probable and definite categories of certainty, which will be of value to the clinician.