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Polycystic Ovarian Syndrome (PCOS) is a common endocrine disorder of reproductive aged women worldwide. It is characterized by anovulation, clinical signs of hyperandrogenism and polycystic ovaries on ultrasound scan. The present study has been planned to establish biomarkers for polycystic ovarian syndrome which confer risk in the development and progression of PCOS. To identify a possible biomarker for PCOS we have analyzed sequence variations in selected candidate genes VEGF, Cx37, Cx43, STAT6 and CDH1. The results showed that the allele and genotype frequency matches for the VEGF, Cx37, Cx43, STAT6 and CDH1genes significantly differ between the cases and healthy age matched controls. the 'G' allele of +405G/C polymorphism of VEGF gene, 'C' allele of C1019T polymorphism in Cx37 gene, 'G' allele of G2964A 3'-UTR Polymorphism in STAT6 gene and -347GA, -160A, +54T alleles of CDH1 gene are significantly elevated in cases than in controls. It reveals that these alleles may increasethe risk of developing PCOS. In conclusion, the sequence variations in the studied candidate genes may have a possible aetiopathological role in the development of PCOS.