Objective: To evaluate how the motor unit number index (MUNIX) is related to high-density motor unit number estimation (HD-MUNE) in healthy controls and patients with amyotrophic lateral sclerosis (ALS). Methods: Both MUNIX and HD-MUNE were performed on the thenar muscles in 18 ALS patients and 24 healthy controls. Patients were measured at baseline, within 2. weeks, and after 4 and 8. months. Clinical evaluation included Medical Research Council (MRC) scale and the ALS functional rating scale (ALSFRS). Results: There was a significant positive correlation between MUNE and MUNIX values in ALS patients (r= 0.49 at baseline; r= 0.56 at 4. months; r= 0.56 at 8. months, all p< 0.05), but not in healthy controls. After 8. months, both MUNE and MUNIX values of the ALS patients decreased significantly more compared to MRC scale, ALS functional rating scale (ALSFRS) and compound muscle action potential (CMAP) (p< 0.05). There was no significant difference in relative decline of MUNIX and HD-MUNE values. Conclusions: In ALS patients, MUNIX and HD-MUNE are significantly correlated. MUNIX has an almost equivalent potential in detecting motor neuron loss compared to HD-MUNE. Significance: MUNIX could serve as a reliable and sensitive marker for monitoring disease progression in ALS. © 2012 International Federation of Clinical Neurophysiology.