Introduction/Aims Motor unit number estimation by F waves (F-MUNE) is an uncommonly used MUNE technique. Our aim in this study was to assess the sensitivity of F-MUNE values elicited with newly developed software in motor neuron diseases. Methods F waves were recorded by 300 submaximal stimuli from abductor digiti minimi and abductor pollicis brevis muscles of 35 patients with amyotrophic lateral sclerosis, 18 with previous poliomyelitis, and 20 controls. The software determined the surface motor unit action potentials (sMUAPs) and calculated the F-MUNE values. Compound muscle action potential scans were also recorded to obtain MScanFit. Results The sMUAP amplitudes were higher and F-MUNE values were lower in both muscles of the patients when compared with controls. F-MUNE values could distinguish patients from controls. Significant correlations were found between F-MUNE and MScanFit in the patient groups. Discussion The new F-MUNE software offered promising results in revealing motor unit loss caused by motor neuron diseases.