Polycystic ovary syndrome the most common gynecological endocrinopathy, is characterized by chronic anovulation and hyperandrogenism. It is commonly noted that people with polycystic ovary syndrome are closely related to obesity and insulin resistance. Several polymorphisms for such conditions have been hypothesized to be involved in its etiology, the present study deals with some of those genes. The main objective of the present study is to investigate the association of the following genes, FTO gene, TCF7L2 gene and PPAR γ gene with Polycystic Ovary Syndrome. In this study the single nucleotide polymorphisms of the above mentioned genes were studied in 30 normal samples and 30 PCOS samples using Tetra-primer amplification refractory mutation system polymer chain reaction (T-ARMS PCR).Among the SNPs analysed, the genotypic and allele frequencies has no significant association with Polycystic Ovary Syndrome. The results showed that no significance was found between the polymorphisms selected in controls and PCOS patients. A few more analysis on a longer cohort will reveal whether thus can be used as a marker for PCOS.