In the past two decades, it has been found that mitochondrial DNA (mtDNA) mutations are associated with a wide range of human diseases, from those affecting single organ to those with multi-system involvement. The purpose of this review is to explore the relationship between mtDNA mutations and human diseases. Four aspects are highlighted: characteristics of mitochondrial genetics, mtDNA mutations in human inherited diseases, role of somatic mtDNA mutations in aging and tumor, as well as diagnosis and treatment of mtDNA diseases.