Background Shoulder pain is a common condition with prevalence estimates of 7–26% and the associated disability is multi-faceted. For functional assessments in clinic and research, a number of condition-specific and generic measures are available. With the approval of the ICF, a system is now available for the analysis of health status measures. The aims of this systematic literature review were to identify the most frequently addressed aspects of functioning in assessments of shoulder pain and provide an overview of the content of frequently used measures. Methods Meaningful concepts of the identified measures were extracted and linked to the most precise ICF categories. Second-level categories with a relative frequency above 1% and the content of measures with at least 5 citations were reported. Results A set of 40 second-level ICF categories were identified in 370 single-item measures and 105 multi-item measures, of these, 28 belonged to activities and participation, 11 to body functions and structures and 1 to environmental factors. The most frequently addressed concepts were: pain; movement-related body functions and structures; sleep, hand and arm use, self-care, household tasks, work and employment, and leisure. Concepts of psycho-social functions and environmental factors were less frequently included. The content overview of commonly used condition-specific and generic measures displayed large variations in the number of included concepts. The most wide-ranging measures, the DASH and ASES were linked to 23 and 16 second-level ICF categories, respectively, whereas the Constant were linked to 7 categories and the SST and the SPADI to 6 categories each. Conclusions This systematic review displayed that measures used for shoulder pain included more than twice as many concepts of activities and participation than concepts of body functions and structures. Environmental factors were scarcely addressed. The huge differences in the content of the condition-specific multi-item measures demonstrates the importance of clarifying the content to select the most appropriate measure both in research and in clinical work. For clinical situations, we propose use of a wide-ranging condition-specific measure that conceptualizes assessments of shoulder pain from a bio-psycho-social perspective. Further research is needed to assess how patient-reported problems in functioning are captured in the commonly used measures.