GALNT2 is a GalNAc transferase that regulates insulin signaling, lipogenesis, and serum lipid fractions. The objective of this study was to investigate the association of GALNT2 rs2144300 and rs4846914 single nucleotide polymorphisms (SNPs) with the risk of polycystic ovary syndrome (PCOS) and related traits. The two SNPs were genotyped in 616 PCOS patients and 482 control subjects. Genetic associations with related traits were also analyzed. The genotype distributions of the two SNPs in PCOS patients were similar to those of normal controls. However, significant differences were noted across the three groups of genotypes with respect to the examined variables. In the PCOS group, subjects with genotype AA at the rs4846914 SNP exhibited an increased fasting serum insulin and homeostasis model insulin resistance (HOMA-IR) index compared with that of corresponding GG or GA genotype carriers (all P < 0.05). When PCOS patients were further separated into obese and non-obese subgroups, the genotype-related effects on insulin and HOMA-IR were more obvious, and variations in BMI and FSH levels were exclusively observed in obese PCOS subjects (all P < 0.05). In addition, fasting plasma glucose levels were affected by the genotypes of the rs2144300 SNP in normal control women (P < 0.05). rs4846914 and rs2144300 polymorphisms in the GALNT2 gene are associated with insulin and HOMA-IR, BMI, and FSH levels in obese PCOS patients and glucose levels in normal control women, respectively, but not with PCOS. GALNT2 rs4846914 AA carrier status may be associated with insulin resistance and related traits in obese patients.