The goal of this dissertation was to establish a magnetic resonance imaging (MRI)-based tracking method for mesenchymal stem cells (MSCs) in ovine and equine models of tendonitis and to apply this method in a longitudinal assessment of cell tracking and tendon healing in vivo.The first aim was designed to establish a labeling method using superparamagnetic iron oxide nanoparticles (SPIOs) in sheep, validate detection limits in vitro and in vivo at 3 Tesla (T), and follow out sheep after injection of labeled cells for 7 and 14 days. Labeled, ovine MSCs remained viable, proliferate, and undergo tri-lineage differentiation and remained detectable in vitro in cell numbers as low as 10,000. Cells remained detectable in vivo by MRI at 7 days, as confirmed by correlative histology for dually labeled SPIO+/GFP+ cells, but cells were not confirmed at 14 days.The second aim was designed to establish a SPIO labeling method in the equine and to validate detection in a clinically relevant model of tendon injury at 1.5 T. Assays indicated no significant changes in cell viability, proliferation, migration, or tri-lineage differentiation due to the presence of SPIOs. Clusters of labeled cells were visible as signal voids in 6/6 subjects. Coalescing regions of signal void were diffusely present in the peritendinous tissues. Greater than expected delocalization of cells was present and relatively few cells were retained within collagenous tendon compared to surrounding fascia. The final aim was to non-invasively monitor cell migration and survival concurrent with healing in an ovine model of acute tendon injury over 28 weeks. SPIO-associated signal dropped off exponentially over the first 6 weeks, but remained present until 28 weeks. Standard deviation (SD) of MRI signal, signal to noise ratios (SNR), and signal difference to noise ratios (SDNR) decreased over time in all subjects. MSC-treated tendons had lower SD, SNR and SDNR than control and SPIO-MSC treated tendons at 28 weeks. Overall, SPIO-labeling appears to be an effective and safe method to label MSCs, although some drawbacks are present. MSC treatment appears to improve tendon healing, but care should be taken when assessing SPIO-labeled cells concurrently with tendon quality.