Henoch-Schönlein purpura (HSP) is the most common systemic vasculitis of childhood. The molecular etiology of HSP is not well understood. The purpose of this study is to investigate the association between polymorphisms in C1GALT1 gene and the risk of HSP in a Chinese population. A total of unrelated 542 northern Chinese were enrolled in this study. PCR-RFLP method was used to genotype the five tagging SNPs in the C1GALT1 gene. Chi-squared test and logistic regression analysis were used for the comparison of genotype distribution between cases and controls. The five tagging SNPs were all in Hardy-Weinberg equilibrium in controls. SNP7 was significantly associated with HSP risk, P = 0.005. The DI genotype, compared with the DD genotype, was associated with a significantly higher risk of developing HSP (OR 1.72; 95 % CI 1.11-2.67). The II genotype, compared with the DD genotype, was associated with a significantly higher risk of developing HSP (OR 3.39; 95 % CI 1.16-9.30). Other SNPs were not associated with HSP risk. Variations in the C1GALT1 gene were found to be associated with HSP risk. Further studies are warranted to validate our findings and to investigate into its underlining mechanism.