['Shoulder arthroplasty provides reliable pain relief and restoration of function. However, the effects of fatty infiltration and atrophy in the supraspinatus and infraspinatus muscles on functional outcomes are not well understood.', 'The purposes of this study were to (1) compare preoperative with postoperative fatty infiltration and atrophy of the supraspinatus and infraspinatus muscles after primary shoulder arthroplasty; and (2) identify any associations between these variables and outcome measures.', 'A retrospective analysis was undertaken of 62 patients with a mean age of 67 years (range, 34-90 years) who underwent shoulder arthroplasty. CT scans were conducted preoperatively and at 12 months postoperatively. Outcome variables included the degree of supraspinatus and infraspinatus fatty infiltration (percent fatty infiltration and Goutallier grade), muscle area (percent muscle area and Warner atrophy grade), shoulder strength, and the Western Ontario Osteoarthritis Score (WOOS), American Shoulder and Elbow Surgeons score, and Constant outcome score.', 'Preoperatively, the mean percent fatty infiltration (FI) within the supraspinatus and infraspinatus was identical at 14%. One year after shoulder arthroplasty, both muscles had less fatty infiltration (6% and 7%, respectively; p<0.001). Similarly, the Goutallier grade significantly improved postoperatively for the supraspinatus (p=0.0037) and infraspinatus (p=0.0007). Conversely, measures of muscle atrophy remained unchanged postoperatively (p>0.251). Preoperatively, greater supraspinatus percent FI was negatively associated with preoperative shoulder strength (r=0.37, p=0.001) and Constant score (r=0.38, p=0.001). Postoperative infraspinatus percent FI was negatively associated with postoperative strength (r=0.3, p=0.021) and Constant score (r=0.3, p=0.04). Multivariable regression analysis of possible predictive factors demonstrated that preoperative supraspinatus percent muscle area (p=0.016) and the diagnosis of osteoarthritis (p=0.017) were associated with better followup WOOS scores, and preoperative supraspinatus strength was associated with postoperative strength (p=0.0024). Higher degrees of preoperative percent FI were not associated with worse patient-reported outcomes postoperatively.'] Are rotator cuff fatty infiltration and atrophy associated with functional outcomes in anatomic shoulder arthroplasty?