BACKGROUND Patients with type 1 diabetes mellitus, myasthenia gravis (MG), and Hashimoto disease are diagnosed as having autoimmune polyendocrine syndrome type 3 (APS3). APS3 is rare, and its pathogenesis is unclear. We describe a female patient with APS3 whose human leukocyte antigen (HLA) type could provide a clue to the pathogenesis of APS3. CASE REPORT A 40-year-old Japanese female patient who had been diagnosed with MG at 5 years of age, and which had been treated with cholinesterase inhibitors, was referred to our hospital with thirst, polydipsia, polyuria, weight loss, and hyperglycemia. She was found to have type 1 diabetes mellitus based on laboratory tests. She was also positive for anti-thyroid peroxidase antibody and was thus diagnosed with Hashimoto disease. This combination of type 1 diabetes mellitus, myasthenia gravis, and Hashimoto disease led to a diagnosis of APS3. Her HLA serotype was A24; B46/54; DR4/9; DQ8/9, and genotype was A*24: 02; B*46: 01: 01/54: 01: 01; C*01: 02; DRB1*04: 06/09: 01: 02; DQB1*03: 02: 01/03: 03: 02; and DQA1*03: 01/03: 02: 01. We subsequently reviewed 10 cases of APS3 combined with MG, including the present case and cases reported in Japanese. This review revealed that HLA-DR9/DQ9 might be a specific HLA subtype associated with APS3 with MG. Four of the 10 cases had MG diagnosed before diabetes mellitus and autoimmune thyroid disease. CONCLUSIONS The present case showed that, in people with HLA-B46 and -DR9, antibody-negative MG can precede the development of APS3 by many years. Physicians should consider the possibility of APS3 when evaluating patients with ocular-type myasthenia gravis, and screen them for type 1 diabetes.