Background: Scapular dyskinesis, characterised by drooping scapulae and reduced upward rotation, has been implicated in the presentation of a number of shoulder disorders. Traditionally, in shoulder rehabilitation programmes, the shrug exercise has been prescribed to facilitate upward rotation of the scapula by strengthening the upper trapezius muscle. The aim of this research was to compare muscle activation levels during the standard shrug and the upward rotation shrug in a normal and pathological population. Methods: Surface electrodes recorded electromyographical activity from upper trapezius, middle trapezius, lower trapezius and serratus anterior muscles in 23 normal participants and 14 participants with multi-directional shoulder instability. Participants completed 10 trials of the standard shrug exercise at 0° of shoulder abduction and the upward rotation shrug exercise at 30° of shoulder abduction in the coronal plane. Muscle activity was expressed as a percentage of maximum voluntary isometric contraction. Findings: The four muscles tested performed at a higher intensity during the modified shrug than the standard shrug. Upper trapezius and lower trapezius activity was significantly greater (P < 0.05) in both populations. Though for middle trapezius and serratus anterior muscles, the modified shrug was statistically significant only in the normal population, P = 0.031 and P = < 0.001 respectively. Interpretation: The upward rotation shrug is a more effective exercise for eliciting muscle activity of the upper and lower trapezius than the standard shrug in a normal and multi-directional instability population. Clinically, the upward rotation shrug might be useful to address scapular dyskinesis involving drooping shoulders and reduced scapula upward rotation.