Analysis of motor unit discharge can provide insight into the neural control of movement in healthy and pathological states, but it is typically completed in one muscle at a time. For some research investigations, it would be advantageous to study motor unit discharge from multiple muscles simultaneously. One such example is investigation of the flexion synergy, an abnormal muscle co-activation pattern in post-stroke individuals in which activation of shoulder abductors is involuntarily coupled with that of elbow and finger flexors. However, limitations in available technology have hindered the ability to efficiently extract motor unit discharge from multiple muscles simultaneously. In this study, we propose the use of high-density surface EMG decomposition from proximal and distal flexion synergy muscles (deltoid, biceps, wrist/finger flexors) in combination with an isometric joint torque recording device in individuals with chronic stroke. This innovative approach provides the ability to efficiently analyze both motor units and joint torques that have been simultaneously recorded from the shoulder, elbow, and fingers. In preliminary experiments, 3 stroke and 5 control participants generated shoulder abduction, elbow flexion, and finger flexion torques at 10, 20, 30 and 40% of maximum torque. Motor unit spike trains could be extracted from all muscles at each torque level. Mean motor unit firing rates were significantly lower in the stroke group than in the control group for all three muscles. Within the stroke group, wrist/finger flexor motor units had the lowest coefficient of variation. Additionally, modulation of mean firing rates across torque levels was significantly impaired in all three paretic muscles. The implications of these findings and overall impact of this approach are discussed.