The aim of the study was to present the prevalence of clinical signs and symptoms among female computer users above 45 years, both in a group with self-reported neck/shoulder trouble (NS cases) and in a group without such trouble (NS controls). The hypothesis was that computer users with self-reported neck/shoulder trouble have more clinical findings than those not reporting trouble, and that a corresponding pattern holds true for physical function. In total 42 and 61 questionnaire-defined NS cases and NS controls participated and went through a clinical examination of the neck and upper extremities and five physical function tests: maximal voluntary contraction (MVC) of shoulder elevation, abduction, and handgrip, as well as endurance at 30% MVC shoulder elevation and a physical performance test. Based on clinical signs and symptoms, trapezius myalgia (38%), tension neck syndrome (17%) and cervicalgia (17%) were the most frequent diagnoses among NS cases, and were significantly more frequent among NS cases than NS controls. A total of 60% of the subjects with reported trouble had one or several of the diagnoses located in the neck/shoulder. Physical function of the shoulder was lower in subjects with self-reported trouble as well as in the subgroup of NS cases with clinical diagnoses. In conclusion, the present clinical diagnoses and physical function tests differed between NS cases and NS controls, and are therefore recommended to be included as quantitative objective measures in assessing musculoskeletal health. Physical function tests should be further developed in order to be able to detect pre-stages of work-related disorders for preventive strategies.