This study explores the hypothesis that high intensity exercise induces degenerative changes in the injury prone equine superficial digital flexor tendon (SDFT) but not in the rarely injured common digital extensor tendon (CDET). The horse represents a large animal model which is applicable to human tendon and ligament physiology and pathology. Twelve age matched, female horses undertook galloping exercise three times a week with trotting exercise on alternative days (high intensity group, n=6) or only walking exercise (low intensity group, n=6) for 18 months. The SDFT, suspensory ligament (SL), deep digital flexor tendon (DDFT) and CDET were harvested from the forelimb. Tissue from the mid-metacarpal region of the right limb tendons was analysed for water, DNA, sulphated glycosaminoglycan and collagen content, collagen type III/I ratios, collagen crosslinks and tissue fluorescence. Left limb tendons were mechanically tested to failure. The analyses showed matrix composition to have considerable diversity between the functionally different structures. In addition the specific structures responded differently to the imposed exercise. High intensity training resulted in a significant decrease in the GAG content in the SDFT but no change in collagen content despite a decrease in collagen fibril diameters (previously published). There were no signs of degeneration or change in mechanical properties of the SDFT. The CDET had a lower water content following high intensity training and a higher elastic modulus. Long term high intensity training in skeletally mature individuals results in changes that suggest accelerated ageing in the injury prone SDFT and adaptation in the CDET.