Polycystic ovary syndrome (PCOS) is accepted as a risk factor for diabetes mellitus, and it is closely related to symptoms such as insulin resistance (IR) and obesity. The study aimed to compare the levels of pro-inflammatory markers Tumor necrosis factor alpha (TNF-α), Interleukin-6 (IL-6), and Interleukin-10 (IL-10), as well as C-reactive protein (CRP), in Polycystic ovary syndrome (PCOS) patients and controls. The association between these genotypes and Body Mass Index (BMI), insulin resistance measurements, and lipid profiles was investigated. In addition, gene polymorphisms will be determined in both groups. The study included 60 subjects divided into two groups. For the patients with PCOS and healthy control groups, the biochemical parameters were measured by the auto analyser, and hormonal, pro-inflammatory parameters were measured using the ELISA method. Serum levels of two groups, TNF-α, IL-6, and CRP, increase significantly. TNF-α, IL-6, and CRP have respective AUC values of 0.763, 0.999, and 1. The AUC value is statistically significant at a 95% confidence level when the p-value for each of the three parameters is less than 0.001. The optimal cut-off values for TNF-α (4.11 pg/ml), IL-6 (2.35 pg/ml), and CRP (1.96mg/l) are determined with a sensitivity of 0.997 and a specificity of 1.00. The total number of biomarkers and these cytokines are significantly correlated. The study concluded that women with PCOS exhibit significantly elevated levels of TNF-α and IL-6 in comparison to the control group. The IL-6 (-174G/C) polymorphism is associated with PCOS and particular metabolic disorders of the syndrome.