Background: Tumor Necrosis Factor Alpha (TNF-α) gene, as an inflammatory factor, plays an important role in reproductive physiology, especially in women with Polycystic Ovary Syndrome (PCOS). Objective: This study aims to investigate the relationship between the -1031 T/C polymorphism of TNF-α gene and biochemical factors in women with PCOS. Methods: In this case-control study, participants were 106 women with PCOS and 114 healthy women referred to Kosar Hospital in Qazvin, Iran. The TNF-α gene’s polymorphism was determined using Polymerase Chain Reaction (PCR) technique and PCR-Restriction Fragment Length Polymorphism (PCR-RFLP) method. Biochemical factors of serum levels were also measured in two groups. Logistic regression analysis examined the relationship between the frequency of alleles in different states and the risk of PCOS. Findings: There were statistically significant difference in the mean levels of total cholesterol, triglycerides, testosterone, two-hour blood glucose and body mass index between the groups, whose values were higher in women with PCOS compared to healthy women (P<0.001). In women with PCOS, the mean serum levels of triglyceride and high-density lipoprotein were significantly different between the three TT, CC, TC genotypes of TNF-α gene polymorphism (P<0.05). The results of regression analysis showed that the TT genotype had significant association with the risk of PCOS (OR=2.43, P=0.006, 95%CI: 1.28-2.62). Conclusion: It seems that there is a relationship between the -1301 (T/C) polymorphism of TNF-α gene and the risk of PCOS in women.