The high incidence of partial rupture of the superficial digital flexor tendor in the equine athlete represents a major cause for concern in the racing industry. Frequently, the lesion is localised to the central core of the tendon. This study tested the hypothesis that the site specific structural failure results from differences in the collagen fibre morphology and associated micromechanics between central and peripheral regions of the tendon. Bundles of collagen fibres were dissected from central and peripheral sites in the mid-metacarpal region of the tendon. Crimp morphology was quantified by polarised light microscopy and mechanical characteristics determined using a fibre tensometer. In older horses, centrally located fibres showed significantly lower values for crimp angle, crimp length and toe limit strain than seen peripherally. There were no significant differences in these features between corresponding sites in the younger horses. No significant difference between sites was found in elastic modulus in either group. These data indicate a non-uniform functional stress distribution which may result from ageing or be related to the exercise history as a feature of accumulated damage. These observations may explain the location of central core lesions seen on clinical examination.