Horses as equine athletes must be conditioned and trained to optimize the whole animal for the particular type of athletic activity. An extremely high proportion of all injuries in the equine athlete in general, and in the racehorse in particular, are associated with the skeletal system, many of which are believed to arise from a mismatch between the prevailing exercise levels and adaptation. To maximize performance, yet minimize injury, it is important to understand and apply the principles of functional adaptation of the component tissues of the skeletal system (bone, cartilage, tendons, and ligaments), which differ in their responses to changes in mechanical environment. With appropriate monitoring owners, trainers, and veterinarians can apply the science underlying functional adaptation to the training of specific equine athletes, and so improve equine welfare.