Juvenile myoclonic epilepsy is a genetically inherited disorder characterized by myoclonic jerks and generalized seizures. It has been proposed that patients with juvenile myoclonic epilepsy have larger motor units (MUs) than normals by MU number estimation and macro electromyography techniques. In this study, an experimental setup for scanning electromyography was built to investigate electrophysiologic cross-sections of the MU territories in 9 patients with juvenile myoclonic epilepsy, 3 patients with spinal muscular atrophy, and 10 healthy volunteers. Scanning electromyography was performed on the biceps brachii muscle. For each MU, three-dimensional maps of the MU territories were plotted. The length of MU cross-section and the maximum amplitude of each MU were measured from these maps and compared among the three groups of subjects. Like spinal muscular atrophy patients, patients with juvenile myoclonic epilepsy had significantly larger MU territories than normal controls.