We present here the rare case of a 73-year-old patient with very late-onset multiple sclerosis who developed autoimmune polyendocrine syndrome (APS)-3. Despite only a few reports describing the association between multiple sclerosis and APS, both of these diseases have been shown to be associated with HLA-DR4. Intriguingly, the HLA genotype profile of this patient included HLA-DR4 which, fine mapped to the DRB1*0405-DQA1*0303-DQB1*0401 extended haplotype, reported to be a susceptibility haplotype for APS-3 in Japan. This unique genetic background might explain the clinical picture of this patient.