Variations in the fat mass and obesity-associated (FTO) gene have recently been associated with obesity and type 2 diabetes mellitus among different ethnic populations. Given that the phenotype of polycystic ovary syndrome (PCOS) overlaps with obesity and type 2 diabetes, we hypothesize that the common rs9939609 variant of FTO gene is related to PCOS susceptibility. We performed a case-control association study on 215 women with PCOS, using 227 healthy women as the control. We examined the association between rs9939609 variant and PCOS susceptibility, as well as between PCOS and obesity-related parameters in Chinese women. We observed significant differences in the allelic and genotypic distributions between PCOS patients and the control group. The A allele was significantly more frequent among PCOS patients than in the control population (15.1% vs. 9.9%; A allele vs. T allele, OR = 1.62, P = 0.019). The A allele carrier genotype (AA and AT) frequencies were also significantly greater in PCOS patients than in the controls (28% vs. 19%; AT and TT vs. TT genotype, OR = 1·61, P = 0.035). In logistic regression, the strength of this association was attenuated after adjustment for body mass index (BMI) (A allele vs. T allele, OR = 1.39, P = 0.286; AT and TT genotypes vs. TT genotype, OR = 1.40, P = 0.312). However, we did not find any significant associations of rs9939609 variant with obesity-related traits. In conclusions, the rs9939609 variant in the FTO gene is associated with PCOS susceptibility in the Chinese population, probably because of its effect on BMI.