Polycystic ovary syndrome (PCOS) is a common hormonal disorder characterized by gonadotropin dysregulation, hyperandrogenism, menstrual irregularity and ovarian morphology. The uncoupling protein-2 (UCP-2) gene is a member of the mitochondrial anion carrier protein (MACP) and is strongly associated with insulin resistance and obesity. An attempt is made to detect the association between PCOS and -866G/A polymorphism in UCP2 gene promoter. The study is carried on forty-seven patients with polycystic ovary syndrome and fifty–six controls. Blood samples were taken for biochemical tests and restriction fragment length polymorphism (RFLP) for detection of -866 G/A UCP2 gene polymorphisms. Significant associations between the -866A/A -866G/A of UCP2 gene promotor and PCOS are reported including a significant association between -866A/A polymorphism of UCP2 and both obesity (high BMI) and type 2 diabetes.