Background The role of degenerative changes in rotator cuff musculature with respect to the functional outcomes of rotator cuff repair have only recently been recognized and are still not well understood. In addition, the reversibility of these changes with repair of the tendons is questionable. Hypothesis Poorer preoperative muscle quality negatively affects outcome, and a successful outcome (in terms of a healed repair) might demonstrate improvements in fatty infiltration and muscle atrophy. Study Design Cohort study; Level of evidence, 2. Methods Thirty-eight patients (mean age, 62 years) were prospectively evaluated with preoperative and 1-year postoperative clinical examination and appropriate magnetic resonance image sequencing to determine grades of muscle atrophy and fatty infiltration of the supraspinatus and infraspinatus muscles. American Shoulder and Elbow Society (ASES), Constant, and pain scores were determined as well as strength measurements. The retear rate and progression of muscle degeneration were also evaluated. Independent predictors of outcome measurements and cuff integrity were determined. Results The overall clinical outcome, including ASES, Constant, and pain scores, improved significantly (P < .0001). Strength in forward elevation improved significantly (P < .006), while external rotation strength did not. There was a strongly negative correlation between muscle quality and outcome results in most cases. When the results were adjusted for multivariate effect, muscle atrophy and fatty infiltration of the infraspinatus muscle were the only independent predictors of ASES and Constant scores (P < .03). Tear size and rotator cuff healing did not play an independent role. Tear size, however, was the only independent predictor of ultimate cuff integrity (P = .002). Both atrophy and fatty infiltration progressed significantly over the course of the study. In cases in which the tendon had re-torn, the progression was found to be more significant than when the repair proved successful (P < .003). Conclusion Muscle atrophy and fatty infiltration of the rotator cuff muscles, particularly of the infraspinatus, play a significant role in determining functional outcome after cuff repair. Tear size appears to have the most influential effect on repair integrity. A successful repair did not lead to improvement or reversal of muscle degeneration and a failed repair resulted in significantly more progression. In general, healed repairs demonstrated minimal progression. These findings suggest that repairs should be performed, if possible, before more significant deterioration in the cuff musculature in order to optimize outcomes, and that understanding the degree of muscle atrophy and fatty infiltration before surgery can help guide patient expectations.