We aimed to identifyHLA-DRB1,-DQA1, and-DQB1alleles/haplotypes associated with European, African, or Native American genomic ancestry (GA) in admixed Brazilian patients with type 1 diabetes (T1D). This exploratory nationwide study enrolled 1599 participants. GA percentage was inferred using a panel of 46 ancestry informative marker-insertion/deletion. Receiver operating characteristic curve analysis (ROC) was applied to identify HLA class II alleles related to European, African, or Native American GA, and showed significant (p< 0.05) accuracy for identifying HLA risk alleles related to European GA: forDRB1*03:01, the area under the curve was (AUC) 0.533; forDRB1*04:01AUC = 0.558, forDRB1*04:02AUC = 0.545. A better accuracy for identifying African GA was observed for the risk alleleDRB1*09:01AUC = 0.679 and for the protective allelesDRB1*03:02AUC = 0.649,DRB1*11:02AUC = 0.636, andDRB1*15:03AUC = 0.690. Higher percentage of European GA was observed in patients with risk haplotypes (p< 0.05). African GA percentage was higher in patients with protective haplotypes (p< 0.05). Risk alleles and haplotypes were related to European GA and protective alleles/haplotypes to African GA. Future studies with other ancestry markers are warranted to fill the gap in knowledge regarding the genetic origin of T1D in highly admixed populations such as that found in Brazil.