Over the last decade, motor unit number estimation (MUNE) methods have been applied with increasing frequency to the study of amyotrophic lateral sclerosis. MUNE is the ideal tool for the assessment of diseases in which the primary defect is motor unit loss, as it enables quantitation and tracking of motor unit numbers while simultaneously gauging countervailing collateral reinervation. These properties make it particularly useful for assessing the effects of both neuroprotective therapies and therapies designed to enhance collateral reinervation, not only in animal models but also in the living patient. Previous studies have supplied important natural history information, confirming an average 50% loss of motor units for every six months of disease progression, and newer pathophysiological investigations are providing unique insight into motor unit behavior in the face of progressive anterior horn cell death. More recent efforts have incorporated MUNE into ongoing, multi-center clinical trials as a putative early biomarker, with encouraging results. As MUNE methods continue to be refined and disseminated, they are proving to be useful and unique tools for the study of motor neuron disease.