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The objective of this systematic review and meta-analysis is to examine which work-related risk factors are associated with specific soft tissue shoulder disorders. We searched the electronic databases of Medline and Embase for articles published between 2009 and 24 March 2016 and included the references of a systematic review performed for the period before 2009. Primary cross-sectional and longitudinal studies were included when outcome data were described in terms of clinically assessed soft tissue shoulder disorders and at least two levels of work-related exposure were mentioned (exposed vs less or non-exposed). Two authors independently selected studies, extracted data and assessed study quality. For longitudinal studies, we performed meta-analyses and used GRADE (Grades of Recommendations, Assessment, Development and Evaluation) to assess the evidence for the associations between risk factors and the onset of shoulder disorders. Twenty-seven studies met the inclusion criteria. In total, 16 300 patients with specific soft tissue shoulder disorders from a population of 2 413 722 workers from Denmark, Finland, France, Germany and Poland were included in the meta-analysis of one case–control and six prospective cohort studies. This meta-analysis revealed moderate evidence for associations between shoulder disorders and arm-hand elevation (OR=1.9, 95% CI 1.47 to 2.47) and shoulder load (OR=2.0, 95% CI 1.90 to 2.10) and low to very low evidence for hand force exertion (OR=1.5, 95% CI 1.25 to 1.87), hand-arm vibration (OR=1.3, 95% CI 1.01 to 1.77), psychosocial job demands (OR=1.1, 95% CI 1.01 to 1.25) and working together with temporary workers (OR=2.2, 95% CI 1.2 to 4.2). Low-quality evidence for no associations was found for arm repetition, social support, decision latitude, job control and job security. Moderate evidence was found that arm-hand elevation and shoulder load double the risk of specific shoulder disorders. Low to very-low-quality evidence was found for an association between hand force exertion, hand-arm vibration, psychosocial job demands and working together with temporary workers and the incidence of specific shoulder disorders.