Methods to monitor transplanted stem cells in vivo are of great importance for potential therapeutic applications. Of particular interest are methods allowing noninvasive detection of stem cells throughout the body. Magnetic resonance imaging (MRI) is a tool that would allow detection of cells in nearly any tissue in the body and is already commonly used in the clinic. MRI tracking of stem cells is therefore feasible and likely to be easily adapted to patients receiving donor cells. Patients with Duchenne muscular dystrophy are good candidates for stem cell therapy, given the naturally regenerative nature of skeletal muscle, which repairs damage by employing endogenous stem cells from the muscle interstitium to regenerate muscle fibers throughout adulthood. We describe methods for labeling stem cells with superparamagnetic iron oxide nanoparticles (SPIO) to enhance MRI contrast, injecting them locally into skeletal and cardiac muscle, or systemically in mouse models for Duchenne muscular dystrophy, and tracking them in muscle tissue of live mice following injection. We focus on the use of whole body MRI to detect stem cells, as this is necessary for conditions such as muscular dystrophy, in which affected tissues are present throughout the body and systemic delivery of stem cells may be necessary. Emphasis is placed on the development of an MRI coil that is field of view (FOV) adjustable and can be used for both whole body imaging to determine stem cell localization as well as subsequent focusing on smaller, local regions where stem cells are present to obtain high-resolution images. We discuss the coil design and its significance for stem cell tracking. We also describe methods for labeling stem cells with a fluorescent dye and for tracking them in postmortem tissue specimens with fluorescent microscopy to correlate, compare, and contrast with results of whole body MRI in preclinical studies.