Women with polycystic ovary syndrome (PCOS) are characterized by excess androgen secretion and anovulatory infertility as a cause of follicular maturation arrest, and they are also associated with insulin resistance and obesity. Recently, it was suggested that one of the etiologies for PCOS is an abnormality of steroid hormones, and excessive secretion of androgen. The endoplasmic reticular cytochrome P450, 17alpha-hydroxylase (CYP17A), plays a key role in the mechanism of steroid hormones such as adrenal and gonadal steroid biosynthesis. Therefore, we studied the association between single nucleotide polymorphisms (SNPs) of the A1 allelic variant of the CYP17 gene and PCOS in a Korean population. The study recruited 134 Korean women with PCOS and 100 healthy women as controls. Using the HapAnalyzer, the genotype of the CYP17A1 polymorphism in PCOS and control patients were analyzed. We considered a p-value lower than 0.05 to be statistically significant. After genotypic analysis, we found seven SNPs of the CYP17A1 gene in a large population of subjects. The frequency of seven SNPs had no significant association with PCOS. However, one haplotype (ht3) had a p-value of p=0.001, suggesting that it may be associated with the pathogenesis of PCOS in a Korean population.