Women with PCOS exhibited significantly higher PPARGC1A promoter methylation and lower mtDNA content; PPARGC1A hypermethylation correlated with IR, waist circumference, and triglycerides. Lower mtDNA content was associated with increased metabolic risk. PCOS patients with metabolic syndrome had greater epigenetic alterations. The gene discussed is PPARGC1A; the disease is polycystic ovary syndrome.