Increasing experimental evidence supports a connection between inflammation and mitochondrial dysfunction. Both acute and chronic inflammatory diseases course with elevated free radicals production that may affect mitochondrial proteins, lipids, and mtDNA. The subsequent mitochondrial impairment produces more reactive oxygen species that further reduce the ATP generation, increasing the probability of cell death. Mitochondrial impairment in now considered a key factor in inflammation because (1) there are specific pathologies directly derived from mtDNA mutations, causing chronic inflammatory diseases such as neuromuscular and neurodegenerative disorders, (2) there are neurodegenerative, metabolic, and other inflammatory diseases in which their progression is accompanied by mitochondrial dysfunction, which is directly involved in the cell death. Recently, a direct implication of mitochondrial reactive oxygen species and, particularly, mtDNA in the innate immune response has been reported. Thus, the mitochondria should be considered targets for new therapies related to the treatment of acute and chronic inflammatory diseases, including the auto-inflammatory ones.