Pernicious anemia is a rare condition characterized by vitamin B12 deficiency anemia due to lack of intrinsic factor, often caused by autoimmune gastritis. Patients with pernicious anemia have a higher incidence of other autoimmune disorders, such as type 1 diabetes, vitiligo, and autoimmune thyroid issues. Therefore, the disease has a clear autoimmune basis, although the genetic susceptibility factors have thus far remained poorly studied. We conduct a genome-wide association study meta-analysis in 2166 cases and 659,516 European controls from population-based biobanks and identify genome-wide significant signals in or near the PTPN22 (rs6679677, p = 1.91 × 10-24, OR = 1.63), PNPT1 (rs12616502, p = 3.14 × 10-8, OR = 1.70), HLA-DQB1 (rs28414666, p = 1.40 × 10-16, OR = 1.38), IL2RA (rs2476491, p = 1.90 × 10-8, OR = 1.22) and AIRE (rs74203920, p = 2.33 × 10-9, OR = 1.83) genes, thus providing robust associations between pernicious anemia and genetic risk factors.