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Patients with amyotrophic lateral sclerosis (ALS) show altered cortical excitability. In this study, we measure modulation of spontaneous motor unit potentials (sMUPs) in hand muscles by multifocal cortical stimulation with a newly developed wearable transcranial rotating permanent magnet stimulator (TRPMS).We conducted cross-sectional and longitudinal electromyographic assessments in 40 and 20 ALS patients, respectively, of the stimulation-induced peak increase in the count of sMUPs in two hand muscles modulated by unilateral TRPMS stimulation of the primary motor cortex. We measured peak sMUP counts during several short sessions consisting of 10 stimuli over 60 s and 30 s post-stimulation periods. The longitudinal component involved an initial assessment at an early stage of the disease and up to five follow-up assessments at least 3 months apart.TRPMS stimulation produced no device-related adverse effects. It showed an inverted V-shaped modulation of the peak sMUP counts as a function of ALS functional rating scale revised scores. The ratios of ALS subjects showing peak sMUP count increases between early and intermediate stages (χ2 = 4.086, df = 1, p = 0.043) and intermediate and late stages (χ2 = 4.29, df = 1, p = 0.038) in cross-sectional data were significantly different. Longitudinal assessment also produced a significant (z = 2.31, p = 0.021) result, with all subjects showing a post-initial visit increase in peak sMUP counts.These results are consistent with delayed onset of upper motor neuronal dysfunction with respect to onset of clinical features. However, the above results need to be confirmed in a larger sample of patients and with multiple lines of evidence.