The study assessed motor unit loss in muscles paralyzed by spinal cord injury (SCI) using a novel compound muscle action potential (CMAP) scan examination. The CMAP scan of the first dorsal interosseous (FDI) muscle was applied in tetraplegia (n=13) and neurologically intact (n=13) subjects. MScanFit was used for estimating motor unit numbers in each subject. The D50 value of the CMAP scan was also calculated. We observed a significant decrease in both CMAP amplitude and motor unit number estimation (MUNE) in paralyzed FDI muscles, as compared with neurologically intact muscles. Across all subjects, the CMAP (negative peak) amplitude was 8.01 ± 3.97 mV for the paralyzed muscles and 16.75 ± 3.55 mV for the neurologically intact muscles (p < 0.001). The CMAP scan resulted in a MUNE of 59 ± 37 for the paralyzed muscles, much lower than 108 ± 21 for the neurologically intact muscles (p < 0.001). No significant difference in D50 was observed between the two groups (p = 0.2). For the SCI subjects, there was no significant correlation between MUNE and CMAP amplitude, or any of the clinical assessments including pinch force, grip force, the Graded Redefined Assessment of Strength, Sensibility and Prehension (GRASSP) score, and SCI duration (p > 0.05). The findings provide an evidence of motor unit loss in the FDI muscles of individuals with tetraplegia, which may contribute to weakness and other hand function deterioration. The CMAP scan offers several practical benefits compared with the traditional MUNE techniques because it is noninvasive, automated and can be performed within several minutes.