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Overhead athletes typically experience anatomical and biomechanical adaptive changes in the dominant shoulders. Adaptations are divided in three main groups: changes in glenohumeral rotator range of motion, malposition and dyskinesis of the scapula, and muscular imbalances between internal and external rotators. Such adaptations, which are physiological at first, can lead to secondary damage of different shoulder structures. Shoulder injuries are among the most common causes for absence from training and competition in overhead sports. Therefore, it is necessary to regularly screen and monitor the development of adaptive changes in each individual. Exercises for preventing the development of adaptive changes must be part of regular preventive training or rehabilitation programmes in case of secondary shoulder injuries. In this review, we describe up-to-date facts about the development of adaptive changes with evidence-based prevention and rehabilitation guidelines.