Immunoglobulin A (IgA) nephropathy (IgAN) is a common form of primary glomerulonephritis characterized by diffuse glomerular mesangial IgA1 deposition leading to mesangial proliferation and chronic glomerular inflammation. Analyses of serum IgA1 from IgAN patients revealed abnormal galactosylation of the O-linked carbohydrate moieties of IgA that may result from altered activity in the core of 1 b1,3-galactosyltransferase (C1GalT1). To evaluate the association between C1GalT1 single nucleotide polymorphisms (SNPs) and IgAN, we performed a case-control study on cohorts from the Uyghur population in China. A total of 180 IgAN patients and 180 healthy controls were recruited for the study. We sequenced 5 SNPs, including SNP1 (rs9639031), SNP2 (-527A/G), SNP3 (rs1008898), SNP4 (rs5882115), and SNP5 (rs1047763) in the C1GalT1 gene in all eligible participants. The frequencies of the I allele and DI genotype of rs5882115 in IgAN patients were significantly higher than those in controls (P < 0.05). The frequency of haplotype GAGDA was significantly higher in patients than in controls (0.0719 vs 0.00, P = 0.024). Polymorphisms in the C1GALT1 gene were associated with genetic susceptibility to Uyghur IgAN.