We present a method called muscle synergy analysis, which can offer clinicians insight into both underlying neural strategies for movement and functional outcomes of muscle activity. Although neural dysfunction is central to many motor deficits, neural activity during movements is not directly measurable. Consequently, the majority of clinical tests focus on evaluating motor outputs at the behavioral and kinematic levels. However, altered behavioral or kinematic outcomes could be the result of multiple distinct neural abnormalities with very different muscle coordination patterns. Because muscle activity reflects motoneuron activity and generates the forces that produce behavioral outcomes, an analysis of muscle activity may provide a better understanding of the functional neural deficits in the impaired nervous system. Unfortunately electromyographic datasets can be large, highly variable, and difficult to interpret, precluding their clinical utility. Computational analyses can be used to extract muscle synergies from such datasets, revealing underlying patterns that may reflect different levels of neural function. These muscle synergies are hypothesized to represent motor modules recruited by the nervous system to flexibly perform biomechanical subtasks necessary for movement. For example, hemiparetic stroke patients exhibit differences in the number of muscle synergies, which may reflect disruptions in descending neural pathways and are correlated to deficits in motor function. Muscle synergy analysis may thus offer the clinician a better view of the neural structure underlying motor behaviors and how they change in motor deficits and rehabilitation. Such information could inform diagnostic tools and evidence-based interventions specifically targeted to a patient's deficits.