In summary, our analysis of 2166 cases and 659,516 controls identifies robust risk loci for pernicious anemia in or near candidate genes with a known role in autoimmune conditions (PTPN22, HLA, IL2RA, and AIRE) and suggests PNPT1 as a potential causal gene with possible sexually dimorphic effects in the 2p16.1 locus that needs further validation. This evidence concerns the gene AIRE and pernicious anemia.