Cell transplantation using hepatocytes derived from stem cells has been regarded as a possible alternative treatment for various hepatic disorders. Recently, mesenchymal stem cells (MSCs) from the bone marrow have shown the potential to differentiate into hepatocytes in in vitro and in vivo conditions. Noninvasive imaging techniques allowing in vivo assessment of the location of cells are of great value for experimental studies in which these cells are transplanted. We labeled human mesenchymal stem cells (hMSCs) with green fluorescence protein (GFP) and superparamagnetic iron oxide (SPIO) using a transfection agent (GenePORTER). Cellular labeling was evaluated with magnetic resonance (MR) imaging of labeled suspensions, and Prussian blue staining for iron assessment. hMSCs labeled with SPIO and GFP were injected into the portal veins of immunosuppressed, hepatic-damaged rats. MR imaging findings were compared histologically. To identify the differentiation of hMSCs into hepatocytes and to trace the hepatocytes with molecular imaging, we observed the potential of SPIO and GFP double-labeled hMSCs to differentiate into hepatocyte-like cells in the regenerating rat liver. Serial MR imaging showed the possible detection of transplanted cells in the early period of transplantation. Our results indicate that magnetic labeling of hMSCs with SPIO may enable cellular MR imaging and tracking in experimental in vivo settings.