The use of Mesenchymal Stromal Cells (MSCs) in orthopedic practice has recently and rapidly acquired an important role. Therapies based on the use of MSCs for the treatment of acute injuries as well as chronic inflammatory disorders are gradually becoming clinical routine. These cells have demonstrated intriguing therapeutic potentialities (i.e.: inflammation control, tissue regeneration and pathological scar prevention), that have been taken into consideration for use in both human and veterinary medicine. In particular, horses represent high performance athletes considered models for human pathologies since musculo-skeletal disorders frequently occur in this species. In the past, repair of tendon injures were performed by different methods. In particular, clinical therapy was based on ice application, bandage, box rest and controlled exercise. An alternative approach consisted on the use of corticosteroid (inflammation reduction) and other drugs (sodium hyaluronate, polysulphated glycosaminoglycans, beta aminoproprionitrile fumarate). Furthermore, surgical treatments like accessory ligament desmotomy, local irritation by line firing or pin firing were commonly used. More recently ultrasound, laser therapy, electromagnetic field therapy have been considered. Unfortunately, they did not allow complete tissue healing and quite often animals did not regain competitiveness. In order to minimize this inconvenience, the use of MSCs has been introduced as an alternative to the traditional approach since it represents a potential tool to improve tissue regeneration. Aim of this study was to evaluate the capability of MSCs to improve the functional outcome of horses affected by tendonitis and desmitis. Thirty-three breed and activity-matched horses affected by tendonitis or desmitis, were included in clinical trial scored for lesions and subdivided into two groups. Group 1 animals were treated with autologous MSCs, associated with platelet rich plasma (group 1). Bone marrow samples were collected from the sternum of the treated horses and processed in order to isolate MSCs. Following cell therapy, they were subjected to a rehabilitation period and their ability to resume training was evaluated. In this study, implanted MSCs caused no adverse reactions and thirteen out of the eighteen inoculated horses returned to race competitions. On the contrary, no improvement was seen in the twelve animals of group 2 treated with pin firing, that were not able to resume sport activity. In conclusion the clinical trial proves the safety of equine bone-marrow derived MSCs and a successful outcome of the treated animals that returned to their previous level of sport activity.