Progress in the development of stem cell and gene therapy requires repeatable and non-invasive techniques to monitor the survival and integration of stem cells in vivo with a high temporal and spatial resolution. The purpose of the present study was to examine the feasibility of using the standard contrast agent gadolinium diethylenetriamine pentaacetic acid (Gd-DTPA) to label rat mesenchymal stem cells (MSCs) for stem cell tracking. MSCs, obtained from the bilateral femora of rats, were cultured and propagated. The non-liposomal lipid transfection reagent effectene was then used to induce the intracellular uptake of Gd-DTPA. Electron microscopy was used to detect the distribution of Gd-DTPA particles in the MSCs. The labeling efficiency of the Gd-DTPA particles in the MSCs was determined using spectrophotometry, and MTT and trypan blue exclusion assays were used to evaluate the viability and proliferation of the labeled MSCs. T1-weighted magnetic resonance imaging (MRI) was used to observe the labeled cells in vitro and in the rat brain. Gd-DTPA particles were detected inside the MSCs using transmission electron microscopy and a high labeling efficiency was observed. No difference was observed in cell viability or proliferation between the labeled and unlabeled MSCs (P>0.05). In the in vitro T1-weighted MRI and in the rat brain, a high signal intensity was observed in the labeled MSCs. The T1-weighted imaging of the labeled cells revealed a significantly higher signal intensity compared with that of the unlabeled cells (P<0.05) and the T1 values were significantly lower. The function of the labeled MSCs demonstrated no change following Gd-DTPA labeling, with no evident adverse effect on cell viability or proliferation. Therefore, a change in MR signal intensity was detected in vitro and in vivo, suggesting Gd-DTPA can be used to label MSCs for MRI tracking.