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Hypothalamic pituitary gonadal axis plays a pivotal role in reproductive physiology, and gonadotropin-releasing hormone 1 (GNRH1) is considered to be the candidate gene in the regulation of the hypothalamic-pituitary-gonadal axis. GNRH1 encodes the pre-proprotein that is processed proteolytically to form the peptide GnRH1. Its polymorphisms may involve in the disruption of the luteinising hormone/follicle-stimulating hormone (LH/FSH) ratio and cause polycystic ovary syndrome (PCOS). The current study investigated the genetic association of rs6185 with PCOS. In addition, <i>in silico</i> analysis and meta-analysis were also performed to clearly understand the role of rs6185 in relation to PCOS. A total of 362 PCOS women and 328 healthy controls were analysed in a case control design. GNRH1 polymorphism rs6185 was genotyped using the ARMS-PCR method. Lipid and hormonal profiles were measured to analyse the correlation between genotype and phenotype. The Chi-square test compared genotypic and allelic frequencies between cases and controls, and the effect was estimated by calculating the Odds ratios at a 95% confidence interval. For meta-analysis, Review Manager 5.4.1 software was used. In the present study, body mass index, waist-to-hip ratio, cholesterol, triglycerides, low-density lipoprotein (LDL), very LDL, LH and LH/FSH ratio were found to be higher in PCOS women. The significant difference in the distribution of the homozygous mutant genotype (GG) and mutant allele (G) of rs6185 was found between PCOS cases and controls (<i>P</i> = 0.047 and 0.037, respectively). The meta-analysis revealed a significant association of the recessive model of rs6185 with PCOS, and <i>in silico</i> predictions confirmed that the rs6185 polymorphism alters the mRNA secondary structure and slightly decreases the stability of protein. The present study demonstrates that there is a significant association of <i>GNRH1</i> polymorphism rs6185 with PCOS.