In the present study, the thenar muscles were evaluated using magnetic resonance imaging (MRI), in addition, the correlations between thenar muscle changes, clinical findings and electrodiagnostic results from patients with carpal tunnel syndrome were investigated. The subjects were 13 patients (17 wrists) who were clinically diagnosed with carpal tunnel syndrome. In all patients, a medical history was obtained and physical examination was performed, in addition to assessment using the Kapandji scoring system, visual analogue scale (VAS), quick-disabilities of the arm, shoulder and hand (Q-DASH) score, electrodiagnostic results of the median nerve, and MRI of the thenar muscles. Thenar muscle volume was not significantly correlated with clinical data or the electrodiagnostic results. The thenar muscle major axis was significantly correlated with grasp power (P<0.05) and the Kapandji score (P<0.05), while the thenar muscle minor axis was significantly correlated with abductor pollicis brevis distal motor latency (APB DML) (P<0.01). In addition, the thenar muscle minor axis/thenar muscle major axis ratio was significantly correlated with APB DML and Kanatani's stage. Notably, thenar muscle thinness was significantly correlated with the severity of electrodiagnostic changes, while the grasp power and Kapandji score were correlated with thenar muscle thickness. Furthermore, it was demonstrated that thenar muscle thinness was significantly correlated with the severity of electrodiagnostic changes; in addition, there was a significant correlation between the thenar muscle major axis and the grasp power or Kapandji score. Taken together, these results revealed that thenar muscle atrophy did not affect patient-based assessments, including VAS and Q-DASH, but reflected electrodiagnostic results, particularly DML and severity. The results of the present study suggest that thenar muscle atrophy can be used to estimate the severity of carpal tunnel syndrome.