Mitochondrial diseases is a group of metabolic disorders caused by abnormal structure and dysfunction of mitochondrial DNA (mtDNA). Abnormalities of mtDNA include point mutations, deletions, and rearrangements and depletion of mtDNA. These may affect the ability of mitochondria to generate energy in cells of various tissues and organs. As many factors are involved in the regulation of mtDNA mutations, most mitochondrial diseases may manifest great genetic heterogeneity and a wide spectrum of clinical manifestations. On the other hand, for the low prevalence of single disease, these disorders may be easily missed or with delayed diagnosis. This review focuses on the pathological mutations and benign variations of mtDNA, and research progress on such disorders.