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Background: Whether vitamin D deficiency is related to rotator cuff muscle and tendon physiology is controversial. Purpose: To assess the relationship between vitamin D deficiency and various gene expression patterns in patients with rotator cuff tears. Study Design: Controlled laboratory study. Methods: During arthroscopic surgery, samples from the supraspinatus muscle, deltoid muscle, and supraspinatus tendon were acquired from 12 patients with vitamin D deficiency (serum 25-hydroxyvitamin D concentration <20 ng/dL) and 12 patients with sufficient vitamin D levels (control group, serum 25-hydroxyvitamin D concentration ≥30 ng/dL) who were matched for age, sex, and tear size. Alterations in the expression of genes and proteins associated with myogenesis, muscle atrophy, adipogenesis, inflammation, and apoptosis, as well as in vitamin D receptor expression, were assessed using quantitative reverse transcription polymerase chain reaction, Western blotting, and immunohistochemistry and were compared between the 2 groups. Results: Vitamin D receptor gene expression in the deltoid muscle was significantly lower in the vitamin D deficiency group than in the control group (P =.043). Additionally, in the deltoid muscle, myoDgene expression levels were lower and atrogin levels were higher in the vitamin D deficiency group than in the control group (P =.034 and P =.011, respectively). However, in the supraspinatus muscle, no differences were observed between groups in the expression of myogenesis- or atrophy-related genes (all P >.05). The expression of inflammation-related genes (interleukin (IL)-1β and IL-6) was significantly higher in the vitamin D deficiency group, in both the deltoid and supraspinatus muscles (all P <.05). The supraspinatus tendon tissue did not show any significant differences in any gene expression evaluated (all P >.05). A correlation between gene and protein expression was observed for atrogin and IL-1β in the deltoid muscle (P =.019 and P =.037, respectively) and for IL-6 in the supraspinatus muscle (P =.044). Conclusion: Vitamin D deficiency was not associated with the expression of myogenesis-related or muscle atrophy–related genes in the supraspinatus muscle of patients with rotator cuff tears, unlike in the deltoid muscle; rather, vitamin D deficiency was associated with increased proinflammatory cytokine expression. Clinical Relevance: In patients with rotator cuff tears, vitamin D deficiency was observed to be associated with increased levels of proinflammatory cytokines in the rotator cuff muscles, without significant changes in gene expression related to myogenesis or muscle atrophy. [ABSTRACT FROM AUTHOR]