Objective: To explore the relationship between axon loss and measured cross-sectional areas of the median nerve (MN) in severe carpal tunnel syndrome (CTS). Methods: In this retrospective study of 158 examined wrists, we compared axon loss to the ultrasound parameters MN cross-sectional area at the wrist (wCSA), MN cross-sectional area at the forearm (fCSA) and wrist-to-forearm ratio (WFR), in patients with moderate to extreme CTS. Axon loss was evaluated by needle electromyography (EMG) of the abductor pollicis brevis muscle (spontaneous activity and reduction of interference pattern). Results: Both the spontaneous activity and interference pattern reduction correlated negatively to fCSA (r = −0.189, p = 0.035; r = −0.210, p = 0.019; respectively). In moderate CTS, both the spontaneous activity and interference pattern reduction correlated positively to WFR (r = 0.231, p = 0.048; r = 0.232, p = 0.047; respectively). The WFR was highest when slight spontaneous activity was detected. Neither wCSA nor WFR correlated with axon loss in severe and extreme CTS. Conclusions: The fCSA is smaller when axon loss in CTS is more prominent. The WFR is highest when CTS is associated with slight axon loss of the MN. Significance: CTS might cause retrograde axonal atrophy detected as small fCSA. Prominent axon loss in CTS may reduce the diagnostic value of WFR.