Background Shoulder pain is a common and often persistent health condition with substantial impact on daily functioning. The primary aim of the present study was to identify important functional problems among patients with shoulder pain, using the Patient-Specific Functional Scale (PSFS). A secondary aim was to investigate differences between primary- and secondary care patients.Methods The study had a cross-sectional design and included patients seeking care for shoulder pain in a primary- and a secondary outpatient clinic. Background variables, pain, physical activity level and the PSFS, were registered with a questionnaire package. Meaningful concepts from the PSFS responses were extracted and linked to the International Classification of Functioning, Disability and Health (ICF), according to the refined linking rules. Frequency for the ICF categories was estimated for primary- and secondary care, separately. Differences between primary and secondary care were investigated by calculating confidence intervals for the sample proportions, at ICF chapter level.Results Of the total 177 patients, 84 were recruited from primary care and 93 from secondary care. The primary care sample reported functional problems linked to 226 ICF categories, while 337 in secondary care. Of the linked ICF categories 87.7% belonged to the Activities and Participation component of the ICF. Seventeen categories were identified in > 3% of the patients, of those the most frequent were: Recreation and leisure (d920), Lifting and carrying objects (d430)’, Doing housework (d640), Hand and arm use (d445) and Remunerative employment (d850). Categories included in the ICF chapters Self-care (d5) and Domestic life (d6) were significantly more frequent in the secondary care sample, while there was a trend that b7 Neuromusculoskeletal and movement-related functions were more frequent in primary care.Conclusion The present findings indicate that patients with shoulder pain report a wide range of functional problems, from basic functions related to mobility to more complex functions related to work and leisure activities. This study also discovered differences in the report of functional problems between primary and secondary care patients. The large variation in the experiences between patients supports the use of an individualised measure to support assessment of functioning among shoulder patients.Trial registration Not applicable