22q11.2 Deletion Syndrome (22qDS) is often complicated by autoimmune diseases. To clarify the causal relationship, we examined the lymphocyte subset distribution and the human leucocyte antigen (HLA) in two female patients (one child and an elderly) with Graves' disease (GD) and 22qDS. Thymus dysgenesis might have contributed to the T-cell imbalance and the lack of negative selection in both cases. Notably, HLA-DR14, a known risk factor for GD in Japanese individuals and the decreased regulatory T-cell numbers that were seen in the pediatric case, may affect the early onset of GD. Central and peripheral tolerance and Th1 cells appeared to be associated with the pathogenesis of GD in 22qDS.