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Motor unit number estimation techniques in amyotrophic lateral sclerosis (ALS) patients are technically challenging and time-consuming. The Motor Unit Number Index (MUNIX) is a novel technique based on surface-EMG recordings and requires only 3-5 minutes per muscle. The objective was to explore the feasibility of longitudinal MUNIX measurements in ALS patients. In seven patients enrolled in a clinical trial, eight muscles were studied every 2 months for up to 15 months in addition to the revised ALS-functional rating scale, slow vital capacity, and compound muscle action potentials. The method was well tolerated and easy to perform. Initial MUNIX measures were significantly reduced compared to controls (487 +/- 194 vs. 1459 +/- 113; P < 0.001). Relative drop from baseline paralleled the clinical course and was greater than the drop of other markers of disease progression. MUNIX measurements in multiple muscles are suitable for serial neurophysiologic investigations in ALS. Further longitudinal data are needed for reliability validation.