Rationale and Objectives: To evaluate the influence of throwing activity on shoulder morphology and the difference in shoulder morphology on MRI between asymptomatic professional baseball players and volunteers who play baseball as a recreational activity. Materials and Methods: This retrospective case-control study included 68 asymptomatic professional baseball players (32 pitchers, 36 batters) and 30 male volunteers. Morphologic changes in the following shoulder structures were assessed on MRI: rotator cuff, glenoid labrum, humeral head, subacromialsubdeltoid bursa, subcoracoid bursa, long head of the biceps tendon, deltoid muscle, acromion, and clavicle. Results: Partially torn supraspinatus, posterior glenoid or labral lesions, bone marrow edema, intraosseous cysts of the humeral head, and edematous subacromial-subdeltoid bursa were significantly more commonly observed in players (p = 0.01, p < 0.001, p = 0.03, p< 0.001, and p < 0.001). Players with more than 10 years of experience had a significantly higher incidence of patchy intermediate signal abnormality (odds ratio: 3.73, p = 0.03), partial tear in the supraspinatus tendon (odds ratio: 6.20, p = 0.03), and edematous change in the subacromial-subdeltoid bursa (odds ratio: 2.96, p = 0.03). Conclusion: The results from our study showed that repetitive throwing activities cause macroscopic structural lesions of the shoulder joints in asymptomatic baseball players. Significance of these lesions is to be determined.