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Little is known of the cellular events that occur in native or repaired tendons as a result of immobilization after injury. To examine this issue, we compared (1) native tendons without immobilization, (2) native tendons with immobilization, and (3) surgically repaired tendons with immobilization.Eighty-one rats underwent either patellar tendon repair followed by immobilization or immobilization of the native tendon without repair. A custom external fixation device was used for immobilization. The tendon-bone insertion site was evaluated after two and four weeks of immobilization with use of histologic, radiographic, and biomechanical analyses.Immobilization of the native tendon led to a significant decrease in the load to failure (p < 0.01) and stiffness (p < 0.05) compared with the native tendon at both two and four weeks. The repaired/immobilized group had a significantly lower load to failure at two weeks compared with the native/immobilized group (p < 0.05); however, by four weeks, the repaired group was significantly stronger (p < 0.01). Micro-computerized tomography demonstrated no significant differences in bone microstructure at two weeks but demonstrated increased bone mineral density and bone volume fraction in the repaired/immobilized group at four weeks. There was significantly more MMP-13 (matrix metalloproteinase-13) staining in the native/immobilized specimens compared with the native specimens at both time points (p < 0.01).Immobilization had a significant detrimental effect on the bone-tendon complex. At two weeks there was a significant decrease in the mechanical properties of the native tendon, but the immobilized, native tendon remained significantly stronger than the repaired and immobilized tendon. However, four weeks of immobilization led to a significant loss of strength of the bone-tendon complex in the native tendon, such that it was significantly weaker than the repaired and immobilized tendon. Surgeons who manage patients with immobilization should be aware of the changes at the bone-tendon complex.Immobilization may have negative effects on the native bone-tendon complex.