Mitochondria are semi-autonomous organelles present in several copies within most
cells in the human body that are controlled by the precise collaboration of mitochondrial DNA
(mtDNA) and nuclear DNA (nDNA) encoding mitochondrial proteins. They play important roles
in numerous metabolic pathways, such as the synthesis of adenosine triphosphate (ATP), the predominant
energy substrate of the cell generated through oxidative phosphorylation (OXPHOS), intracellular
calcium homeostasis, metabolite biosynthesis, aging, cell cycles, and so forth. Previous
studies revealed that dysfunction of these multi-functional organelles, which may arise due to mutations
in either the nuclear or mitochondrial genome, leads to a diverse group of clinically and genetically
heterogeneous disorders. These diseases include neurodegenerative and metabolic disorders
as well as cardiac and skeletal myopathies in both adults and newborns. The plethora of
phenotypes and defects displayed leads to challenges in the diagnosis and treatment of mitochondrial
diseases. In this regard, the related literature proposed several diagnostic options, such as
high throughput mitochondrial genomics and omics technologies, as well as numerous therapeutic
options, such as pharmacological approaches, manipulating the mitochondrial genome, increasing
the mitochondria content of the affected cells, and recently mitochondrial diseases transmission
prevention. Therefore, the present article attempted to review the latest advances and challenges in
diagnostic and therapeutic options for mitochondrial diseases.