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This review deals with the state of the art in knowledge about molecular diagnostics in mitochondrial diseases. A considerable development over the last years of several lines of biological, biochemical and biophysical investigation techniques has enormously enlarged the chance to obtain significant information by their application in the study of mitochondrial diseases in both in vivo and in vitro clinical applied research. The nosography of mitochondrial diseases is, therefore, day by day enriched by reports of new acquisitions that merge with the innovative contribution that novel laboratory and clinical investigative technologies add to the knowledge of the physiopathology and management of these complex diseases. Apart from the molecular genetic characterization of mitochondrial diseases, different experimental laboratory approaches have contributed, from a molecular point of view, to add new insights in this field of medicine. The strategies of these investigations can be targeted to detect and evaluate the significance of molecules that can play a relevant role in the determination of clinical phenotypes, making it possible to better understand several still unexplained mechanisms of cell damage. [ABSTRACT FROM AUTHOR]