Abstract Background Polycystic ovary syndrome (PCOS) is an endocrine-metabolic disorder that affects women at their child bearing age. The exact etiology is uncertain, however the involvement of multiple genes and environmental interactions has been proposed for the advancement of PCOS. The aim of present study was to evaluate the association of LHCGR variants (rs2293275 and rs12470652) with PCOS in Punjab. Methods The present case–control study comprised a total of 743 women (421 PCOS cases and 322 healthy controls). Genotyping was performed using polymerase chain reaction-restriction fragment length polymorphism technique (PCR–RFLP). Biochemical analysis was carried out to measure the levels of cholesterol, High-density lipoprotein (HDL), Low-density lipoprotein (LDL), Very low-density lipoprotein (VLDL), triglycerides, testosterone, luteinizing hormone (LH) and follicle-stimulating hormone (FSH). All the statistical analysis was done using SPSS (version21, IBM SPSS, NY, USA). Results The mutant genotype (AA) and mutant allele (A) of rs2293275 conferred 1.7 and 1.3 fold risk, respectively and mutant allele (C) of rs12470652 conferred 2.3 fold risks towards PCOS progression. Levels of cholesterol and triglycerides were elevated and HDL levels were lower in PCOS cases as compared to controls. Total testosterone and luteinizing hormone levels were also found to be higher in PCOS cases. Conclusion Our study postulated that LHCGR variants are playing a cardinal role in the progression of PCOS and can be used to assess the risk of PCOS in women of reproductive age.