More than 30% of the population over age 60 will suffer from a rotator cuff tear. Progressive tears lead to atrophic and degenerative muscle changes that persist irrespective of therapeutic intervention, whether conservative or surgical. The degree of decreased muscle quality (retraction, atrophy, fibrosis, and fatty degeneration) serves as the strongest predictor of post-surgical functional outcomes, yet the quantitative effects on muscle physiology are poorly understood. The purpose of this work was to investigate the structural and functional implications of rotator cuff tear and repair in a rabbit model system. We first established a method to evaluate the structure-function relationship in healthy supraspinatus muscles. We then performed a detailed architectural analysis to relate the structural and physiological consequences of rotator cuff tear and repair. Finally, we evaluated the activation of mechanotransduction pathways in our model system to investigate a potential mechanism for persistent muscle loss. In summary, we characterized aspects of the altered structure-function relationship in both torn and surgically repaired rotator cuff muscles to better understand the physiological implications of disease and potential therapies.