Examination of the shoulder complex has long been described as challenging. This is particularly true in the examination of the overhead athlete who has structural differences when compared to a shoulder patient who is a non‐athlete. Complexity with the examination is due to unique biomechanical and structural changes, multiple joint articulations, multiple pain patterns, and the potential of injury to structures both inside (intra‐articular) and outside (extra‐articular) the glenohumeral joint. Repetitive stresses placed on the shoulders of overhead athletes may affect range of motion, strength, scapular position, and ultimately, the integrity of soft tissue and bony structures in any of the joints that comprise the shoulder complex. Furthermore, many shoulder examination tests thought to be unique to a single structure, joint, or condition can be positive in multiple conditions. The examination of the overhead athletes shoulder, coupled with a thorough medical history will provide a solid foundation to allow a functional physical therapy diagnosis and provide clues as to the presence of the lesion (s) causing disability. The purpose of this clinical commentary is to assist the reader to understand the unique physical characteristics of the overhead athlete, which will lead to a more accurate and reproducible evaluation of athletes who sustain injuries while participating in overhead sports.