Polycystic Ovarian Syndrome (PCOS) is the most common endocrine disorder of women in their reproductive ages. Though PCOS is a complex, heterogeneous disorder, but there is strong evidence for its genetic predisposition. The aim was to study the association of Follicle Stimulating Hormone Receptor (FSHR) gene polymorphisms rs1394205, rs6165 and rs6166 in south Indian women with PCOS. The present case control study includes 97 women with PCOS and 101 healthy women without any history of infertility. Polymerase chain reaction and Restriction fragment length polymorphism based method were applied to identify the genotypes. Distribution of alleles and genotypes did not differ significantly between PCOS and controls (p-value: >0.05). Genotypic association analysis shows a significant association of rs6166 (G/G) genotype with PCOS in recessive gene model (P value: 0.04). Haplotype frequencies and their association analysis did not show any significant difference between PCOS and controls. No strong linkage is observed between rs6165 and rs6166 in the present study. Our study reveals significant association of FSHR gene polymorphism, rs6166 with PCOS in recessive gene model. When we observe the genotype frequencies, high frequency of heterozygotes in the population shows that rs6166 (G/A) in heterozygote condition is advantage to the population.