Allogeneic Hematopoietic stem cell transplantation (allo-HSCT) is effective for several diseases, including leukemia, solid tumors, and immunodeficiency. However, there are still some intractable diseases that cannot be treated with HSCT alone. We have developed a new HSCT method, allo-HSCT + thymus transplantation (TT) from the same donor, which induces elevated T cell function with mild graft-versus-host disease (GVHD) in comparison to conventional HSCT alone and HSCT + donor lymphocyte infusion (HSCT + DLI). This method leads to improvement of immune function and the ability of engraftment, and is effective for treatment of autoimmune chronic pancreatitis and sialoadenitis in aging, lupus nephritis in hosts with radioresistance, and supralethal irradiation, in which conventional HSCT alone is ineffective. This method may become a valuable form of clinical therapy for intractable diseases.