Disorders of the shoulder are extremely common, with reports of prevalence ranging from 30% of people experiencing shoulder pain at some stage of their lives up to 50% of the population experiencing at least one episode of shoulder pain annually. In addition to the high incidence, shoulder dysfunction is often persistent and recurrent, with 54% of sufferers reporting ongoing symptoms after 3 years. To a large extent the substantial morbidity reflects (i) a current lack of understanding of the pathoaetiology, (ii) a lack of diagnostic accuracy in the assessment process, and (iii) inadequacies in current intervention techniques. Pathology of the rotator cuff and subacromial bursa is considered to be the principal cause of pain and symptoms arising from the shoulder. Generally these diagnostic labels relate more to a clinical hypothesis as to the underlying cause of the symptoms than to definitive evidence of the histological basis for the diagnosis or the correlation between structural failure and symptoms. Diagnosing rotator cuff tendinopathy or subacromial impingement syndrome currently involves performing a structured assessment that includes taking the patient's history in conjunction with performing clinical assessment procedures that generally involve tests used to implicate an isolated structure. Based on the response to the clinical tests, a diagnosis of rotator cuff tendinopathy or subacromial impingement syndrome is achieved. The clinical diagnosis is strengthened with the findings from supporting investigations such as blood tests, radiographs, ultrasound, magnetic resonance imaging (MRI), computed axial tomography (CT), radionucleotide isotope scan, single photon emission computed tomography, electromyography, nerve conduction and diagnostic analgesic injection. This process eventually results in the formation of a clinical hypothesis, and then, in conjunction with the patient, a management plan is decided upon and implemented. This paper focuses on the dilemmas associated with the current process, and an alternative method for the clinical examination of the shoulder for this group of patients is proposed.