Autoimmune polyglandular syndrome (APS) type 2 is defined by the manifestation of at least two autoimmune endocrine diseases. Only few data exist on genetic associations of APS type 2. In this controlled study, 98 patients with APS type 2, 96 patients with type 1 diabetes (T1D), and 92 patients with autoimmune thyroid disease, both as a single autoimmune endocrinopathy, were tested for association with alleles of the human leukocyte antigen (HLA) class II loci DRB1, DQA1, and DQB1. Patients with APS type 2 had significantly more often the alleles DRB1*03 (P_c < 0.0001), DRB1*04 (P_c < 0.000005), DQA1*03 (P_c < 0.0001), and DQB1*02 (P_c < 0.05), when compared with controls. Less frequent in APS were DRB1*15 (P_c < 0.05), DQA1*01 (P_c < 0.0005), and DQB1*05 (P_c < 0.005). With regard to frequency and linkage of these alleles, the susceptible haplotypes DRB1*0301‐DQA1*0501‐DQB1*0201 and DRB1*0401/04‐DQA1*0301‐DQB1*0302 were deduced. Protective haplotypes in this study were DRB1*1501‐DQA1*0102‐DQB1*0602 and DRB1*0101‐DQA1*0101‐DQB1*0501. Comparing APS patients with vs without AD, no significant differences regarding HLA class II alleles were noted in our collective. Patients with T1D as a singular disease had the same susceptible and protective HLA alleles and haplotypes. The prevalence of DRB1*03 and DRB1*04 in APS patients was not because of the presence of diabetes, as the APS type 2 patients without diabetes had the same allele distribution. In conclusion, these data suggest a common immunogenetic pathomechanism for T1D and APS type 2, which might be different from the immunogenetic pathomechanism of other autoimmune endocrine disease.