The value of motor unit number estimation (MUNE) in determining the prognosis of acute peripheral facial paralysis (PFP) was evaluated in 89 patients with PFP on days 6, 8, 11, 14, 20, and 30 of PFP and repeated once per month until complete recovery or the end of the first year. The symptomatic/asymptomatic side ratios of the compound muscle action potential (CMAP) amplitudes recorded from nasalis muscles and MUNEs studied using the incremental method by recording from the same muscle were assessed with regard to three outcome groups (Group I, complete recovery; Group II, mild dysfunction; Group III, moderate-moderately severe dysfunction). CMAP and MUNE ratios were parallel to each other in all patient groups throughout the observation period with lower values in the more severe groups. However, CMAP amplitude loss was significantly greater than the MUNE loss in the first 3 weeks of PFP. The MUNE method is not superior to CMAP size in determining prognosis in PFP. However, the significant disparity between the CMAP and MUNE ratios in the early period may have some physiological relevance with regard to the pathophysiology of the Wallerian degeneration process and deserves further research into its potential sources.