Since the innate immune system can influence the disease activity of myasthenia gravis (MG), such as during infection, the frequencies of natural killer (NK) cells and NKT cells were analyzed in the blood and thymus. Before therapy (thymectomy plus glucocorticoid), the MG patients with thymic hyperplasia, but not those with thymoma, showed increased frequencies of mature NKT cells (CD3(+)TCRV(alpha)24(+)CD161(bright)) in the blood, while the frequency of immature NKT cells was unaltered. In the blood of the patients with thymoma, but not those with hyperplasia, the frequency of cytotoxic subclass of NK cells (CD3(-)CD16(+)CD56(dim)) was lower than that of the control. These alterations returned to normal after therapy. The thymic frequencies of NKT cells and NK cells in MG thymuses were unaltered. These results suggest the involvement of both innate and acquired immunity in the disease activity of MG.