To determine the association of clinical and electrophysiological findings in cases of carpal tunnel syndrome (CTS) using motor unit (axon) number estimation (MUNE) of the median nerve and to evaluate how these findings can contribute to treatment planning. Material and Methods: Evaluation was made of 43 hands of 25 patients (22 females, 3 males, mean age 45.63±9.89 years) with clinical and electrophysiological diagnosis proven CTS and a healthy control group of 50 hands of 25 subjects (21 females, 4 males, mean age 44.72±8.89 years). Electrophysiological nerve transmission measurements and CTS grading were applied. MUNE measurement was made from the abductor pollicis brevis (APB) muscle with the incremental method. Results: According to the electrophysiological grading, the mean MUNE values were at Grade-0: 134.66±41.00, Grade-1: 78.83±33.51, Grade-2: 71.72±32.15 and Grade-3: 50.25±27.45. A positive correlation was determined between electrophysiological grading and APB muscle atrophy, and median nerve latency. A negative correlation was determined with MUNE, muscle strength, median nerve amplitude and conduction velocity. Between MUNE and muscle strength, median nerve amplitude and conduction velocity there was a positive correlation, between MUNE and median nerve latency, a negative correlation was found. According to regresion analysis, median nerve wrist segment sensory velocity and median nerve distal motor action potential amplitude were predictive parameters for MUNE. Conclusion: Together with the clinical evaluation, patients with grade 3 and/or MUNE value below 2 standard deviations of normal according to the electrophysiological evaluation, should be considered for surgery, while in milder cases, it can be recommended that clinical and electrophysiological follow-up is added to conservative treatment.