The trapezius is a muscle of clinical interest due to its susceptibility to chronic work related musculoslteletal disorders. The mechanisms underlying these conditions are not fully understood. A comprehensive and comparative biochemical characterization of the trapezius muscle may reveal particular individual traits that make it more susceptible to chronic work related musculoskeletal disorders. We have examined the suitability and outcome of a proteomic method, two-dimensional difference gel electrophoresis (2D-DIGE), in the analysis of human skeletal muscle. This method allows a simultaneous comparison of large numbers of proteins within a limited pH and molecular weight range. A protocol using the 2D-DIGE method was adapted to human muscle and its repeatability was tested on human vastus lateralis muscle samples from one healthy male donor. The vastus lateralis is the most well studied muscle in the human body and was therefore used as the gold standard. The method was validated using western blot technique. Subsequently, a comparative 2D-DIGE analysis using the validated protocol was conducted on vastus lateralis and trapezius muscle biopsies from five healthy male subjects. Proteins were identified using matrix assisted laser desorption ionisation time of flight (MALDI-TOF) mass spectrometry and immunohistochemistry was performed on serial sections to confirm the findings. The 2D-DIGE method proved to be a good screening tool to further detect biochemical differences between muscles. The comparative study between the trapezius and vastus lateralis demonstrated significant differences in 25 important metabolic and structural proteins. In particular, it showed differences in proteins related to oxidative stress, which may be of specific importance for the susceptibility of the trapezius muscle to work related musculoskeletal disorders. These results provide a baseline for future studies on the trapezius muscle and puts further emphasis on the differences between different types of skeletal muscle.