Increasing evidence points to the importance of aberrant O-glycosylated immunoglobulin A1 (IgA1) in the pathogenesis of IgA nephropathy (IgAN), a disease widely considered to be a polygenic disorder. We earlier found that haplotypes in two key glycosyltransferase genes, C1GALT1 and ST6GALNAC2, were associated with susceptibility to IgAN. Here we measured the genetic interaction of variants in C1GALT1 and ST6GALNAC2 by applying FAMHAP software to analyze haplotype-haplotype interaction in IgAN. As confirmation, we also used a novel divergence-based multi-locus algorithm (DBMA) approach to determine interactions between single-nucleotide polymorphisms. Haplotype-haplotype combinations in C1GALT1 and ST6GALNAC2 were significantly associated with a predisposition for IgAN and with the estimated glomerular filtration rate (eGFR) of patients. Analogously, results from DBMA found a five-locus combination, two in ST6GALNAC2 and three in C1GALT1, which was associated with IgAN predisposition, eGFR, and renal outcome of patients with IgAN. In addition, patients with a high risk had significantly more exposed N-acetylgalactosamine on their IgA1 than did patients with a lower risk of developing this disease. Our findings suggest that potential genetic interactions of C1GALT1 and ST6GALNAC2 variants influence IgA1 O-glycosylation, disease predisposition, and disease severity, and may contribute to the polygenic nature of IgAN.