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Objective: To investigate the frequency of Pro12 Ala polymorphism in PPAR gamma gene among PCOS of south Indian population. Understanding this polymorphism may help us in better diagnosis prevention and therapeutic approaches towards management of PCOS. Method: A total of 75 women with the diagnosis of PCOS and 75 healthy controls were included in this study. The Pro 12 Ala variant in the PPAR gamma gene was analysed by PCR-RFLP. Results: Genotypic frequencies for PPAR gamma gene Pro12 Ala polymorphism showed the frequency of Pro/Pro genotypes was 77% in PCOS and 81% in controls. The odds ratio was 0.71 (95% CI 0.31-1.63) and 2.66 (95% CI 0.21-32.9) and alleles expressed 0.87 (95% CI 0.42-1.79). Regarding hormone levels, there were significant differences between PCOS and non PCOS. Conclusion: PPARγ2 gene Pro12Ala polymorphism was supposed to be susceptible genes in PCOS. The present study demonstrated that there is a statistical difference between the distributions of PPAR gamma Pro12Ala polymorphism in South Indian Population.