Several hypotheses regarding the underlying mechanisms and the maintenance behind chronic work-related musculoskeletal disorders have been presented. Chronic low load work and psychosocial stress is believed to be the underlying causes to these pain conditions. The recent application of comprehensive screening methods: omnics methods; to this field of research could contribute to current knowledge regarding the pathophysiology of these disorders. The pathophysiological mechanisms behind chronic trapezius myalgia are discussed in the context of new findings obtained with proteomic and metabolomic methods. Proteins and metabolites which differ in abundance between healthy muscle and muscle suffering from chronic trapezius myalgia are presented. Primarily, the pathways and effects of the proteins and metabolites found in three recently published papers are discussed. Proteomics and metabolomics are efficient screening methods enabling the presentation of potential biomarkers and pathophysiological mechanisms explaining the pathophysiology of chronic work-related trapezius myalgia. The previous findings detecting systematic differences of proteins and metabolites when comparing chronic myalgic muscle to healthy muscle, indicating a higher glycogen metabolism, increased muscle turnover and increased neuronal signalling in the myalgic muscle, are discussed in this review.