Polycystic ovary syndrome (PCOS) is a disorder characterized by hyperandrogenism, chronic oligoanovulation and insulin resistance. A number of women with PCOS are obese and exhibit abnormal phenotypes, including high levels of androgens, an irregular menstrual cycle and increased hair growth. Studies on obese PCOS patients have proven the crucial role that obesity plays in insulin resistance and hyperinsulinemia. The uncoupling protein (UCP) gene is one of the genes known to have a strong association with obesity and insulin resistance. Thus, we analyzed the association between the -866G/A polymorphism in the promoter of UCP2 and PCOS. Genotyping was performed by polymerase chain reaction along with restriction fragment length polymorphism analysis, followed by an analysis of the genotype of the UCP2 polymorphism in PCOS and control subjects using HapAnalyzer. The study included samples from 277 PCOS patients and 152 healthy controls. P<0.05 was considered to be statistically significant. In conclusion, no association was found between the -866G/A single nucleotide polymorphism and PCOS (P=0.7168, OR=1.07, 95% CI). The present study showed that -866G/A, a UCP2 gene polymorphism, is not associated with the pathogenesis of PCOS.