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Background: The clinical implications of structural integrity have been a subject of long debate. The oversimplified binary categorization of structural integrity into either healing or retear, along with faulty preoperative baselines for comparison, may contribute to the controversy. Purpose: To determine how the quality of structural integrity in a repaired cuff tendon affects both clinical and structural outcomes by dividing the patients into groups based on integrity and using the immediate postoperative baseline (time zero). Study design: Cohort study; Level of evidence, 3. Methods: A total of 504 patients with a full-thickness rotator cuff tear who underwent arthroscopic rotator cuff repair and were followed up for at least a year with magnetic resonance imaging (MRI) were included. The quality of structural integrity was graded using the Sugaya classification. To evaluate clinical outcomes, pain, range of motion, strength, functional scores, and overall satisfaction and function were used for within- and between-group analyses at the last follow-up. For the assessment of structural outcomes, the Goutallier classification for fatty infiltration (FI) and the tangent sign, occupation ratio, and normalized cross-sectional area for muscle atrophy (MA) were used. The baselines for these structural measurements were both the preoperative and the time-zero MRI scans. Results: The mean clinical follow-up period was 31.8 ± 27.5 months, and the MRI follow-up period was 10.9 ± 5.3 months. There were 178 (35.3%), 228 (45.2%), 58 (11.5%), 14 (2.8%), and 26 (5.2%) shoulders with Sugaya grades 1, 2, 3, 4, and 5, respectively. Regardless of structural integrity, all clinical outcomes at a mean follow-up of 31.8 months after repair significantly improved compared with those before repair. Only in shoulders with Sugaya grade 1 did the FI of the supraspinatus muscle improve significantly from baseline. FI of the infraspinatus muscle did not change significantly in those with grades 1 and 2 but worsened in those with grades 3 and 5. MA measured using the occupation ratio improved significantly in shoulders with Sugaya grades 1 and 2 but declined in those with grade 5. Conclusion: This study established a correlation between improved structural integrity of the repaired cuff tendon and enhanced structural outcomes in rotator cuff muscles. Furthermore, the findings revealed that both FI and MA could be reversed in patients exhibiting high-quality structural integrity. However, these structural improvements were not mirrored in the clinical outcomes. [ABSTRACT FROM AUTHOR]