Analysis of disease-causing mutations in mitochondri genome requires rapid and reliable genetic approaches. However, the preparation of mitochondrial DNA (mtDNA) probe used for the determination of quantitative and qualitative mtDNA defects is time-consuming, cumbersome, and requires complicated instrumentation. To overcome the difficulties encountered during isolation and purification of mtDNA, the authors developed an alternative method based on polymerase chain reaction (PCR) amplification of whole mtDNA genome. In this study, they show that PCR-amplified and fluorescein-labeled mtDNA probe makes it possible, through Southern blot analysis, to identify quantitative defect of mtDNA. The results indicate that mtDNA probe can be prepared rapidly by PCR amplification and used to determine the level of mtDNA in the patients with mitochondrial diseases.