Specific tendons show a high incidence of partial central core rupture which is preceded by degeneration. In the performance horse, the superficial digital flexor tendon (SDFT) is most often affected. We have described previously the molecular changes that are associated with degeneration in the central core region of the equine SDFT. The pathophysiological mechanism leading to change in synthetic activity of central zone cells in degenerated tendons is not known. In this study, we test the hypothesis that ageing results in matrix composition changes within the central zone of the SDFT. Extracellular matrix composition and cellularity were analysed in equine SDFTs collected from Thoroughbred horses and compared with a flexor tendon which rarely shows degenerative change and subsequent injury (deep digital flexor tendon, DDFT). Data were examined for age-related changes to central and peripheral zone tissue of the SDFT and DDFT. Ageing in both tendons (SDFT and DDFT) resulted in a significant increase in collagen-linked fluorescence and a decrease in cellularity in the DDFT but not the SDFT. The central zone tissue from the SDFT had a significantly higher proportion of type III collagen than the peripheral zone of the tendon. The highest level of type III collagen was found in the central zone tissue of the SDFT from the older group of horses and this may represent the early stages of a degenerative change. Collagen content did not differ between the 2 flexor tendons; however, there were differences in collagen type and organisation. The SDFT had a higher type III collagen content, higher levels of the mature trifunctional collagen crosslink hydroxylysylpyridinoline, lower total chondroitin sulphate equivalent glycosaminoglycan content, smaller diameter collagen fibrils and a higher cellularity than the DDFT. In conclusion, differences in macromolecular composition exist between the flexor tendons and ageing contributes to a tendon specific change in composition.