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Objective To compare transverse and longitudinal safe zones using ultrasonography between healthy individuals and patients with carpal tunnel syndrome (CTS). Methods This was a prospective observational case-control study. Forty wrists from 20 healthy individuals and 40 wrists from 24 patients with CTS were examined. Patients with CTS were classified into three groups (mild, moderate, and severe CTS) based on electrodiagnostic findings. Using ultrasonography, we measured the distance between the median nerve and ulnar vessels to identify the transverse safe zone, and between the distal flexor retinaculum and superficial palmar artery arch to identify the longitudinal safe zone. Results The transverse and longitudinal safe zones were significantly different between participants with CTS and those without CTS. The transverse safe zone significantly differed between the mild and severe CTS groups, while the longitudinal safe zone was not significantly different between the groups. The cross-sectional area of the median nerve negatively correlated with the transverse and longitudinal safe zones. Conclusion Transverse and longitudinal safe zones were narrower in patients with CTS than in the healthy group. A significant difference was observed between patients with mild CTS and those with severe CTS. Furthermore, the cross-sectional area of the median nerve was directly proportional to the degree of narrowing of the transverse and longitudinal safe zones.