The objective of this paperwas to characterize complex neuromuscular changes induced by a hemisphere stroke through a novel clustering index (CI) analysis of surface electromyogram (EMG). The CI analysis was performed using surface EMG signals collected bilaterally from the thenar muscles of 17 subjects with stroke and 12 age-matched healthy controls during their performance of varying levels of isometric muscle contractions. Compared with the neurologically intact or contralateral muscles, mixed CI patterns were observed in the paretic muscles. Two paretic muscles showed significantly increased CI implying dominant neurogenic changes, whereas three paretic muscles had significantly reduced CI indicating dominantmyopathic changes; the other paretic muscles did not demonstrate a significant CI alternation, likely due to a deficit of descending central drive or a combined effect of neuromuscular factors. Such discrimination of paretic muscles was further highlighted using a modified CI method that emphasizes between-side comparison for each individual subject. The CI findings suggest that there appears to be different central and peripheral processes at work in varying degrees after stroke. This paper provides a convenient and quantitative analysis to assess the nature of neuromuscular changes after stroke, without using any special equipment but conventional surface EMG recording. Such assessment is helpful for the development of appropriate rehabilitation strategies for recovery of motor function.