BACKGROUND: In cell therapy, magnetic resonance imaging (MRI) has been used to visualize superparamagnetic iron oxide (SPIO)-labeled stem cells homing to a lesion. Improving traceability is to utilize the sequence that maximizes sensitivity to the susceptibility effect of SPIO. PURPOSE: To explore the best method by comparing the MRI sequences to visualize mesenchymal stem cells (MSCs) labeled with SPIO. MATERIAL AND METHODS: Human bone marrow (hBM)-derived MSCs were labeled by internalization of SPIO nanoparticles. In vitro MRI was performed for the SPIO-labeled hBM-MSCs in tubes with T2-weighted (T2W), T2*-weighted (T2W), and susceptibility-weighted images (SWI). Contrast-to-noise ratio (CNR) and volumes of dark signal of SPIO-labeled hBM-MSCs were obtained on images of each sequence. Photothrombotic cerebral infarction (PTCI) was induced in eight rats, and 2.5 × 10(5) SPIO-labeled hBM-MSCs were infused through the tail vein on the third day. In vivo MRI of the rat brain was performed using a 3.0 T MRI on the first, third, seventh, and 14th days. CNRspio was obtained on T2W imaging, T2W imaging, and SWI. The dark signals were compared with the SPIO-positive cells of Prussian blue staining. RESULTS: In vitro MRI of 5 × 10(5) SPIO-labeled hBM-MSCs showed the CNR and volume of dark signal to be 63, 517 mm(3) in SWI, 41, 228 mm(3) in T2W imaging, and 56, 41 mm(3) in T2W imaging, respectively. In vivo MRI showed a dark signal surrounding the high signal intensity of PTCI. Pathologically, the dark signals were matched with SPIO-labeled hBM-MSC in the corresponding rat. The dark signal was most prominent in SWI, then T2W imaging, and finally in T2W imaging (P <0.05). In SWI, other causes of dark signals were matched with the veins and the choroid plexuses on histopathology. CONCLUSION: SWI can visualize SPIO-labeled hBM-MSCs more sensitively, earlier, and with larger size and greater contrast than T2W imaging and T2*W imaging.