Optimal management of tendon overuse injuries in equine and human athletes should avoid the formation of excessive scar tissue, regenerate normal tendon matrix, and reduce re-injury rates. We hypothesized that the implantation of marrow-derived stromal stem cells (BM-MSCs), in far greater numbers than are present normally within tendon tissue, would synthesize a matrix more closely resembling tendon matrix than scar tissue, and hence increase the capacity to return to performance successfully. This article reviews the technique used clinically in the horse and the current outcome data for horses treated by the autologous implantation of BM-MSCs into moderate to severe acute superficial digital flexor tendon (SDFT) injuries. Bone marrow was aspirated from the sternum under standing sedation. The nucleated adherent cell population (containing the BM-MSCs) were isolated and expanded so that, after approximately three weeks, the cells were re-suspended in the supernatant from the bone marrow and implanted into injured SDFT under ultrasonographic guidance. The horses then entered a 48-week rehabilitation period consisting of an ascending exercise regime. By September 2006, 168 racehorses had undergone this regimen. For horses which had returned to full work, 18% had re-injured, which compared favourably to previous studies on conventional management (56% re-injury rate). No adverse effects were noted other than needle tracts visible ultrasonographically. Autologous implantation of mesenchymal stem cells into tendon injuries may therefore improve clinical outcome although definitive proof of efficacy, which is still lacking, will require randomized controlled trials.