We have previously found that conventional allogeneic bone marrow transplantation (allo BMT) can be used to treat various spontaneously developed autoimmune diseases in mice. In addition, we have found that autoimmune diseases can be transferred into the normal mice by conventional BMT from autoimmune-prone mice. Based on these findings, we have proposed that autoimmune diseases are "stem cell disorders." To apply allo BMT to humans, we extensively carried out BMT to clarify which cells are essential for successful BMT, and finally found that three types of cells are essential for successful allogeneic BMT: (1) hemopoietic stem cells (HSCs), (2) natural suppressor cells, and (3) stromal cells (including mesenchymal stem cells, MSCs). We have very recently found that MSCs play a crucial role in preventing graft failure, since there is a major histocompatibility complex restriction between HSCs and MSCs. To recruit donor-derived MSCs, we have found that the injection of whole bone marrow cells into the bone marrow cavity (intra-bone marrow-BMT, IBM-BMT) is the best strategy for the treatment of various otherwise intractable diseases, including autoimmune diseases. In this review article, we provide evidence that IBM-BMT heralds a revolution in the field of transplantation and regeneration medicine.