Mucosa-associated lymphoid tissue (MALT) lymphoma in the thymus is extremely rare, and little is known about its clinicopathological features. In this study, we examined four cases of MALT lymphoma in the thymus at our institute in terms of clinicopathological features. Most patients had autoimmune disease or hyperglobulinemia, and they also had cysts in the tumors. Both elevated serum levels of autoantibodies and the polyclonal increase in serum Ig remained almost unchanged after total thymectomy in all patients. We recommend that MALT lymphoma in the thymus should be considered in the differential diagnosis when a cystic thymic mass is found and if the patient is Asian and/or has autoimmune disease or hyperglobulinemia.