We studied a large North American Caucasian population of patients with biopsy proven IgA nephropathy for polymorphisms of HLA-A,B,C, HLA-DR, HLA-DQ and HLA-DP using a combination of serologic phenotyping and polymerase chain reaction sequence specific oligonucleotide probe (PCR-SSOP) hybridization genotyping. We also examined patients for polymorphisms of immunoglobulin by determing Gm and Km allotypes. When compared to healthy local controls there was an apparent decrease in HLA-DR5 (DRw11, DRw12) suggesting that this allele had a protective effect on disease susceptibility. None of the previously reported HLA-DQ associations found among Japanese or British Caucasian patients were found among this large North American Caucasian population. The HLA-DPB1*0601 genotype was increased among patients, but this was not significant when corrected for multiple comparisons. There were no differences in the distribution of Gm or Km allotypes among patients versus controls, regardless of whether they were stratified into those with progressive or non-progressive renal disease. Taken together, these findings suggest that there is substantial genetics heterogeneity in susceptibility to IgA nephropathy among different ethnic and/or geographically distinct populations.