Background Malunion of the clavicle with shortening after mid shaft fractures can give rise to long-term residual complaints. The cause of these complaints is as yet unclear. Methods In this study we analysed data of an earlier experimental cadaveric study on changes of shoulder biomechanics with progressive shortening of the clavicle. The data was used in a musculoskeletal computer model to examine the effect of clavicle shortening on muscle function, expressed as maximal muscle moments for abduction and internal rotation. Findings Clavicle shortening results in changes of maximal muscle moments around the shoulder girdle. The mean values at 3.6 cm of shortening of maximal muscle moment changes are 16% decreased around the sterno-clavicular joint decreased for both ab- and adduction, 37% increased around the acromion-clavicular joint for adduction and 32% decrease for internal rotation around the gleno-humeral joint in resting position. Interpretation Shortening of the clavicle affects muscle function in the shoulder in a computer model. This may explain for the residual complaints after short malunion with shortening. Level of evidence Basic Science Study. Biomechanics. Cadaveric data and computer model