Background: To assess subclinical involvement of shoulder joints in patients with rheumatoid arthritis (RA) by using musculoskeletal ultrasound (MSUS) and detect their predictors. Results: We found 75% of the patients have subclinical ultrasound changes in their shoulder joints where 65% of the patient’s shoulders are affected. About 57.5% of the shoulder joints showed peri-articular structural changes by ultrasound, while the articular changes were 36.9% with the most frequent one being supraspinatus tendinopathy (43.12%) followed by subacromial-subdeltoid bursitis [total (31.87%), effusion (16.87%), and synovial hypertrophy (15%)], supraspinatus tendon partial tear (30.62%), and long head of biceps tenosynovitis (effusion only) (28.75%), while the least frequencies were glenohumeral joint erosion (11.25%) and synovitis (12.5%). Older age and longer disease duration were significant predictors for the peri-articular changes with p value < 0.5, while high disease activity, seropositive rheumatoid factor, and long disease duration were significant predictors for the articular changes with p value < 0.5. Conclusion: Although shoulders were clinically silent in RA patients, we found a high percentage of subclinical abnormalities detected by MSUS, which were more predominant in the peri-articular structures. MSUS is a simple and non-invasive technique that can be used to detect RA shoulder subclinical affection.