We have established new bone marrow transplantation (BMT) methods for the treatment of stem cell disorders such as autoimmune diseases. The methods include the perfusion method (PM) and intra-bone marrow (IBM)-BMT. PM, in comparison with the conventional aspiration method, can minimize the contamination of bone marrow cells (BMCs) with T cells from the peripheral blood. Therefore, without removing T cells, no graft-versus-host disease develops in the case of PM. Because BMCs collected using the PM contain not only hemopoietic stem cells (HSCs) but also mesenchymal stem cells (MSCs), the injection of both cells directly into the bone marrow cavity (IBM-BMT) facilitates the engraftment of donor hemopoietic cells. With IBM-BMT, no graft failure therefore occurs even if the radiation dose is reduced. IBM-BMT is applicable to regeneration therapy and various age-associated diseases such as osteoporosis, because it can efficiently recruit donor-derived normal MSCs into the bone marrow. We believe that this strategy heralds a revolution in the field of transplantation and regenerative therapy.