Rotator cuff tears are the leading cause of shoulder pain and shoulder-related disability and account for 4.5 million physician visits in the United States annually. A careful history and structured physical examination are often sufficient for diagnosing rotator cuff disorders. We are not aware of a clinical review article that presents a structured physical examination protocol of the rotator cuff for the interested clinician. To fill this void, we present a physical examination protocol developed on the basis of review of prior literature and our clinical experience from dedicated shoulder practices. Our protocol includes range of motion testing by using a goniometer, strength testing by using a dynamometer, and select special tests. Among the many tests for rotator cuff disorders that have been described, we chose ones that have been more thoroughly assessed for sensitivity and specificity. This protocol can be used to isolate the specific rotator cuff tendon involved. The protocol can typically be completed in 15 minutes. We also discuss the clinical implications and limitations of the physical examination maneuvers described in our protocol. This protocol is thorough yet time efficient for a busy clinical practice. It is useful in the diagnosis of rotator cuff tears, impingement syndrome, and biceps pathology.