Whether stroke-induced paretic muscle changes vary across different distal and proximal muscles remains unclear. The objective of this study was to compare paretic muscle changes between a relatively proximal muscle (the biceps brachii muscle) and two distal muscles (the first dorsal interosseous muscle and the abductor pollicis brevis muscle) following hemisphere stroke using clustering index (CI) analysis of surface electromyograms (EMGs). For each muscle, surface EMG signals were recorded from the paretic and contralateral sides of 12 stroke subjects versus the dominant side of eight control subjects during isometric muscle contractions to measure the consequence of graded levels of contraction (from a mild level to the maximal voluntary contraction). Across all examined muscles, it was found that partial paretic muscles had abnormally higher or lower CI values than those of the healthy control muscles, which exhibited a significantly larger variance in the CI via a series of homogeneity of variance tests (p < 0.05). This finding indicated that both neurogenic and myopathic changes were likely to take place in paretic muscles. When examining two distal muscles of individual stroke subjects, relatively consistent CI abnormalities (toward neuropathy or myopathy) were observed. By contrast, consistency in CI abnormalities were not found when comparing proximal and distal muscles, indicating differences in motor unit alternation between the proximal and distal muscles on the paretic sides of stroke survivors. Furthermore, CI abnormalities were also observed for all three muscles on the contralateral side. Our findings help elucidate the pathological mechanisms underlying stroke sequels, which might prove useful in developing improved stroke rehabilitation protocols.