Red blood cell (RBC) auto-immunization poses a clinical dilemma, because the formation of RBC autoantibodies in certain patients is a significant causative factor for autoimmune hemolytic anemia. To clarify whether specific HLA-DRB1 and HLA-DQB1 alleles are associated with the response to RBC auto-immunization, we conducted a case-controlled retrospective study. The case group included 117 patients with autoantibodies potentially harmful to RBC after transfusion at the Beijing Red Cross Blood Center, and the controls were 1.6 million healthy subjects whose data are stored in the China Marrow Donor Program database. In the case group, the frequencies of HLA-DRB1 and HLA-DQB1 allele were determined by PCR-rSSO Luminex high-resolution technology. HLA-DRB1*13 allele expression was not detected in the 75 autoantibody positive patients with anti-C3d production (adjusted P=0.0383), whereas the presence of HLA-DRB1*14 allele showed a positive correlation with the autoantibody positive group with anti-C3d production (odds ratio = 2.22, 95% confidence interval = 1.293.84, adjusted P=0.0383). The HLA-DQB1*02 allele was more frequent in patients with both RBC auto-antibodies and alloantibodies. There was no significant association between a positive antiglobulin test result and the presence of HLA-DRB1 and HLA-DQB1 alleles. In summary, we found that HLA-DRB1*13 may serve as a protective factor, whereas HLA-DRB1*14 appears to be a risk factor for the production of autoantibodies positive with anti-C3d in RBC auto-immunization. To our knowledge, this is the first study to propose HLA-DRB1*13 as a protective factor in auto-immunization.