Rehabilitation following injury or surgery for the athlete who employs overhead motion is extremely challenging. Shoulder pathophysiology and the repetitive intense demands required during athletic activity need to be fully appreciated for successful rehabilitation. This article discusses new anatomic and biomechanical concepts that require the rehabilitation specialist to reconsider previously accepted notions. Treatment rationale is discussed based on these concepts. Rehabilitation principles and phases are described in a sequentially progressive program based on tissue reactivity and signs and symptoms.