Stem cell therapy has been used to repair ischemic tissues in the limbs, in myocardial infarctions, and in the brain. To understand the mechanisms of healing, a contrast agent capable of inducing sufficient magnetic resonance (MR) contrast would be useful in providing fundamental information about the cell migration and incorporation into the ischemic tissue. A magnetic resonance imaging contrast agent composed of dextran and gadolinium chelate was synthesized. Hydroxyl groups of dextran were activated with 1,1'-carbonylbis-1H-imidazole and reacted with propanediamine to obtain aminated dextran. This modified polymer was then reacted with mono-N-succinimidyl 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetate, then with fluorescein isothiocyanate, and finally reacted with gadolinium chloride solution (Dex-DOTA-Gd3(+)). Endothelial progenitor cells (EPCs) were selected as a stem cell model for magnetic resonance imaging tracking. Cells were isolated from the bone marrow harvested from the femurs and tibias of rats. Dex-DOTA-Gd3(+) was then introduced into the EPCs by electroporation. The intracellular stability and cytotoxicity of Dex-DOTA-Gd3(+) were evaluated in vitro. Dex-DOTA-Gd3(+)-labeled EPCs were transplanted into a rat model of ischemic limb, and MR images were acquired. Dex-DOTA-Gd3(+) was found to efficiently label EPCs over a long duration without significant cytotoxicity. This provides an MR signal sufficient for tracking the EPCs intramuscularly injected into the limb.