Abstract Background The most prevalent nerve entrapment disorder, known as carpal tunnel syndrome (CTS), is brought on by wrist-based median nerve compression. Focal demyelination progresses to axonal dysfunction as the condition worsens. In order to detect motor unit (MU) loos, this study compares two motor unit number estimation (MUNE) techniques with compound muscle action potential (CMAP) amplitude. The CMAP amplitude and MUNE of the median nerve in 137 hands of 70 neurophysiologically approved CTS patients, aged 40.27 ± 10.06 years were examined. Another 90 hands from 56 healthy volunteers who are age- and gender-matched serve the control group. Results In contrast to 192.5 and 248.5 in controls, the median nerve values of incremental and adapted multipoint stimulation (aMPS) MUNE in CTS patients were, respectively, 111 and 133 (p