The aim of this study is to conduct in vivo, noninvasive magnetic resonance imaging of labeled rat bone mesenchymal stem cells (BMSCs) as they home into the site of injured common carotid artery following allograft transplantation. Our study was approved by the Institutional Committee on Animal Research. Purified rat BMSCs were dual labeled with superparamagnetic iron oxide (SPIO) particle and fluorescent DiI dye, and subsequently transplanted into recipient rats injured in the left common carotid arteries. Immediately before and 3 hr, 3, 7 and 12 days after transplantation, the labeled cells were monitored in vivo using a 7T micromagnetic resonance imaging (7T micro-MRI) scanner. The signal-to-noise ratios (SNRs) at the injured sites were corroborated with histological examination using Prussian blue staining and fluorescent imaging. Rat BMSCs were labeled with SPIO and DiI at 100% efficiency. When compared with the baseline level before transplantation, the SNR decreased significantly on Days 3 and 7 after injection in the experimental group (Dunnet t test, P < 0.05), whereas insignificant differences were observed after 3 hr and 12 days (Dunnet t test, P > 0.05). In the control group, no significant differences in SNR were found among different time points (ANOVA, P > 0.05). Histological analyses illustrated that red fluorescence and Prussian blue-positive cells were mainly distributed around the lesion areas of injured common carotid arteries. Rat BMSCs can be efficiently labeled with SPIO and DiI, and the directional homing of labeled cells to the site of injured common carotid arteries after intravascular transplantation could be tracked in vivo with 7T micro-MRI.