The objective of this study was to assess whether there is evidence of motor unit loss in muscles paralyzed by spinal cord injury (SCI), using a measurement called motor unit number index (MUNIX). The MUNIX technique was applied in SCI (n=12) and neurologically intact (n=12) subjects. The maximum M waves and voluntary surface electromyography (EMG) signals at different muscle contraction levels were recorded from the first dorsal interosseous (FDI) muscle in each subject. The MUNIX values were estimated using a mathematical model describing the relation between the surface EMG signal and the ideal motor unit number count derived from the M wave and surface EMG measurements. We recorded a significant decrease in both maximum M wave amplitude and in estimated MUNIX values in paralyzed FDI muscles, as compared with neurologically intact muscles. Across all subjects, the maximum M wave amplitude was 8.3±4.4 mV for the paralyzed muscles and 14.4±2.0 mV for the neurologically intact muscles (p <; 0.0001). These measurements, when combined with voluntary EMG recordings, resulted in a mean MUNIX value of 112±71 for the paralyzed muscles, much lower than the mean MUNIX value of 228±49 for the neurologically intact muscles (p <; 0.00001). A motor unit size index was also calculated using the maximum M wave recording and the MUNIX values. We found that paralyzed muscles showed a mean motor unit size index value of 80.7±17.7 μV, significantly higher than the mean value of 64.9±10.1 μV obtained from neurologically intact muscles (p <; 0.001). The MUNIX method used in this study offers several practical benefits compared with the traditional motor unit number estimation technique because it is noninvasive, induces minimal discomfort due to electrical nerve stimulation, and can be performed quickly. The findings from this study help understand the complicated determinants of SCI induced muscle weakness an- provide further evidence of motoneuron degeneration after a spinal injury.