Mechanical testing of connective tissues such as tendons and ligaments can lead to collagen denaturation even in the absence of macroscale damage. The following tensile loading protocols, ramp loading to failure, overloading and release, cyclic overloading and cyclic fatigue loading, all yield molecular damage in rat or bovine tendons. Single collagen fibrils extracted from the positional common digital extensor tendon of the forelimb also show molecular damage after tensile loading to failure. Using fibrils from the same source we assess changes to the molecular and supramolecular structure after tensile stress relaxation at strains between 4 and 22% followed by release. We observe no broken fibril and no significant change in D-band spacing. However, we observe significant binding of a fluorescent collagen hybridizing peptide to the fibrils indicating that collagen denaturation occurs in a strain dependent way for relaxation times between 1 s and 1500 s. We also show that peptide binding is associated with a decrease of the cross-sectional area of the fibrils providing an estimate of the dry volume loss due to molecular denaturation as well as an estimate of the mechanical energy density required, 25-110 MJ m-3. In summary we show that collagen molecular damage can occur in the absence of fibril failure and without visible changes to the supramolecular structure.