OBJECTIVE: We analyzed quantification of mitochondria DNA (mtDNA) to investigate the relationship of mitochondria and pathogenesis of PCOS. MATERIALS AND METHODS: Peripheral blood samples were collected from 28 patients with PCOS who were under the inclusion criteria for PCOS and from 28 healthy controls. Genomic DNA was used to analyze real-time PCR for mtDNA copy number quantification. The mtDNA copy number was compared between the control and PCOS groups. All data was expressed as mean +/- SD. Statistical analysis was assessed by t-test. RESULTS: In this study, the mtDNA CT was 11.67+/-0.422 in PCOS patients and 11.51+/-0.722 in control group, respectively. The mtDNA copy number was 1726410.71+/-407858.591 the patients of in PCOS and 2167887.51+/-252459.28 in control group (p=0.08), respectively. CONCLUSION: In our study, using real-time PCR, there was a tendency of lower mtDNA copy number in the patients of PCOS when comparing to the control group even though statistical difference was not significant. However, more extensive analysis is required to clarity relationship between mtDNA copy number and pathogenesis of PCOS.