Abstract We report a microfluidic system for automatic mitochondrial mutation diagnostics from sample purification to quantitative analysis. The system achieved direct DNA (mtDNA) mutation quantification in affected cells using a new 3D-microfluidic system, which integrated a mtDNA extraction module and a mutation detection module. Effective direct mtDNA extraction from the cells was realized using magnetic field manipulation. The obtained mtDNAs were subject to a fully automatic processing for quantitative mutation detection using integrated micropumps, micromixer and microtemperature control modules capable of mutation sensing by restriction enzyme digestion and real-time on-chip micro-PCR. Compared with traditional methods, this microfluidic system demonstrates the advantages of faster detection, requirement of fewer amount of specimens and reagents, much compact design and lower cost as well as lower risks for human errors. Thus, such system-on-chip would encourage the future translational development of rapid pathogenic mtDNA defects detection to provide more efficient clinical diagnosis and disease management strategies.