Mesenchymal stem cells (MSC) have special characteristics such as migration into the damaged tissues and undergoing differentiation. One of the ways for tracking MSC in the tissue is labeling cells by contrast agents such as superparamagnetic iron oxide (SPIO) and detection by magnetic resonance imaging (MRI). To study adverse effects of SPIO on labeled cells, the formation of apoptosis in labeled cells was investigated using the comet assay. MSC were grown in vitro and labeled with various doses of SPIO for various time intervals. Incorporation of iron in cells were verified both microscopically and atomic absorption spectrophotometer. Labeled cells in a sandwich of low and normal melting agarose on slides were subjected to electrophoresis. The slides were stained with ethidium bromide and analysed under a fluorescent microscope. Results show that SPIO at various doses (50-250 microg/mL) in conjunction with protamine sulphate, used as a cationic transfection agent; and treatment times of 24-72 h did not statistically affect the frequency of apoptosis in labeled MSC (p>0.05). These findings therefore, may be indicative that labeling stem cells using these agents should facilitate the translation of this method to clinical trials for evaluation of trafficking of infused or transplanted cells by MRI.