The goal in the therapeutic use of mesenchymal stem cells (MSCs) in musculoskeletal disease is to harness the regenerative nature of these cells focussing on their potential to grow new tissues and organs to replace damaged or diseased tissue. Laboratory isolation of MSCs is now well established and has recently been demonstrated for equine MSCs. Stem cell science has attracted considerable interest in both the scientific and clinical communities because of its potential to regenerate tissues. Research into the use of MSCs in tissue regeneration in general reflects human medical needs, however, the nature, prevalence and prognosis of superficial digital flexor tendonitis has put equine veterinary science at the forefront of tendon regeneration research. Much has been investigated and learnt but it must be appreciated that in spite of this, the field is still relatively young and both communities must prepare themselves for considerable time and effort to develop the technology into a highly efficient treatments. The promise of functional tissue engineering to replace old parts with new fully justifies the interest. At present, however, it is important to balance the understanding of our current limitations with a desire to progress the technology.