Tendons can be considered in two functional groups, those contributing to energetics of locomotion and those acting solely to position the limb. The energy storing tendons in both human and equine athletes have a high frequency of injury with similar pathophysiology. In previous studies, high intensity exercise appears to induce a disruption of the matrix rather than functional adaptation in adults. Here we explore the hypothesis that the introduction of controlled exercise during growth would result in an adaptive response without deleterious effects. Young horses were given a controlled exercise programme similar to that previously shown to induce matrix changes in energy storing tendons of skeletally mature animals. The tendons were assessed in relation to mechanical properties, molecular composition and morphology. Results showed a significant increase in Cartilage Oligomeric Matrix Protein (COMP) in the positional tendon but not in the energy storing tendon. Other matrix properties and mechanical properties were not significantly changed. While the imposition of high strain rate exercise in immature horses failed to augment the development of the energy storing tendon over and above that induced by normal pasture exercise, it did not induce deleterious changes, supporting an earlier introduction of athletic training in horses.