The present study was aimed to clarify the proliferation capacity of the bone marrow stromal cells (BMSC) transplanted into the brain. The BMSC were harvested from green fluorescence protein (GFP)-transgenic mice, grown to the confluency and passed three times. They were labeled by co-culture with Ferucarbotran, a superparamagnetic iron oxide (SPIO) agent. The proportions of the SPIO-positive cells were evaluated from P3 to P7, using Turnbull blue staining. The GFP-BMSC labeled by Ferucarbotran were transplanted into the ipsilateral striatum of the mice brain subjected to permanent focal ischemia at 7 days after the insult. The distribution and differentiation of GFP- and SPIO-positive cells in the brain were studied 3 months after transplantation, using immunohistochemistry and Turnbull blue staining. As the results, the proportions of the SPIO-positive cells gradually decreased from 93.6% at P3 to 6.5% at P7. Fluorescence immunohistochemistry revealed that the GFP-positive cells were widely distributed around infarct and partially expressed MAP2 and NeuN 3 months after transplantation. However, only a smaller number of SPIO-positive cells could be detected on Turnbull blue staining. The ratio of the SPIO- to GFP-positive cells was approximately 2.7%. The results strongly suggest that the BMSC repeat proliferation many times, migrate into the lesion, and partially express the neuronal phenotype in the host brain during 3 months after transplantation. The double labeling technique would be valuable to prove the proliferation of the transplanted cells in the host tissue because GFP gene and SPIO nanoparticles have different inheritance characteristics.