Rotator-cuff injury (RCI) represents 50% of shoulder injuries, and prevalence increases with age. Even with successful tendon repair, muscle and joint function may not return.To explore the dysfunction, supraspinatus and ipsilateral deltoid (control) muscles were biopsied during arthroscopic RCI repair for pair-wise histological and protein-expression studies.Supraspinatus showed fiber atrophy (P < 0.0001), fibrosis (by Sirius Red, P = 0.05), reduced vascular density (P < 0.001), and a lower proportion of slow fibers (P < 0.0001) compared with the ipsilateral control muscle. There were also higher levels of atrogin-1 (P = 0.05), vascular endothelial growth factor (VEGF, P < 0.01), and dystrophin (P < 0.008, relative to fiber diameter) versus control.Adaptive changes in vascular endothelial growth factor and dystrophin were likely associated with reduced vascular supply, fatigue resistance, and fibrosis, accompanied by disuse atrophy from mechanical unloading of supraspinatus after tendon tear. Treatment to promote growth and vascularity in atrophic supraspinatus muscle may help improve functional outcome after surgical repair. Muscle Nerve 55: 715-726, 2017.