Background Motor unit number estimation (MUNE) can directly assess motor neuron populations in muscle and quantify the degree of physiologic and/or pathologic motor neuron degeneration. A high degree of reproducibility and reliability is required from a good quantitative tool. MUNE, in various ways, in being increasingly applied clinically and statistical MUNE has several advantages over alternative techniques. Nevertheless, the optimal method of applying statistical MUNE to improve reproducibility has not been established. Methods: We performed statistical MUNE by selecting the most compensated compound muscle action potential (CMAP) area as a test area and modified the results obtained by weighted mean surface-recorded motor unit potential (SMUP). Results: MUNE measures in amyotrophic lateral sclerosis (ALS) patients showed better reproducibility with size-weighted modification. Conclusions: We suggest size-weighted MUNE testing of "neurogenically compensated" CMAP areas present an optimal method for statistical MUNE in ALS patients.