We established a new magnetic targeting system in which bone marrow stromal cells migrate through the cerebrospinal fluid to the desired site in the spinal cord in rats. Subarachnoid injection has been reported as a minimally invasive method of transplantation of bone marrow stromal cells for spinal cord injury. It may be, however, less effective than direct injection into the spinal cord in terms of cell delivery. After implantation of a magnet, subarachnoid injection of bone marrow stromal cells labeled with magnetic beads was performed. Greater numbers of bone marrow stromal cells aggregated on the surface of the spinal cord owing to the magnetic force. This targeting system may be a useful tool in minimally invasive transplantation of bone marrow stromal cells for the treatment of spinal cord injury.