Mitochondria DNA (mtDNA) plays an important role in both aging-associated degenerative diseases and cancers. In this study, a new microfluidic system integrating functional components including a mtDNA extraction module, a polymerase chain reaction (PCR) module and a micro-capillary electrophoresis (MCE) module has been developed. A new approach to vertically integrate these three modules has been reported. A cell lysis device, pneumatic micropumps, and an active micromixer were first used for fast extraction of mtDNA from cells. Then, the PCR and the MCE modules were used for nucleic acid amplification and separation of mtDNA. Experimental data showed that the deletion of mtDNA can be automatically detected with this approach.