The overhead throwing motion is an extremely skillful and intricate movement that is very stressful on the shoulder joint complex. The overhead throwing athlete places extraordinary demands on this complex. Excessively high stresses are applied to the shoulder joint because of the tremendous forces generated by the thrower. The thrower's shoulder must be lax enough to allow excessive external rotation, but stable enough to prevent symptomatic humeral head subluxations, thus requiring a delicate balance between mobility and functional stability. We refer to this as the "thrower's paradox." This balance is frequently compromised, which leads to injury. Numerous types of injuries may occur to the surrounding tissues during overhead throwing. Frequently, injuries can be successfully treated with a well-structured and carefully implemented nonoperative rehabilitation program. The key to successful nonoperative treatment is a thorough clinical examination and accurate diagnosis. Athletes often exhibit numerous adaptive changes that develop from the repetitive microtraumatic stresses observed during overhead throwing. Treatment should focus on the restoration of these adaptations during the rehabilitation program. In this article, the typical musculoskeletal profile of the overhead thrower and various rehabilitation programs for specific injuries are discussed. Rehabilitation follows a structured, multiphase approach with emphasis on controlling inflammation, restoring muscle balance, improving soft tissue flexibility, enhancing proprioception and neuromuscular control, and efficiently returning the athlete to competitive throwing.