Thumb opposition does not always represent the function of the median nerve due to variations in thenar muscle innervation. One hundred and thirty hands of 109 idiopathic carpal tunnel syndrome (CTS) patients with an undetectable compound muscle action potential of the abductor pollicis brevis (APB-CMAP) were classified into one of four groups; Type 1 (86.2%) had thenar muscle atrophy and could not perform thumb opposition; Type 2 (10.8%) had thenar muscle atrophy but could perform thumb opposition; Type 3 (2.3%) did not have thenar muscle atrophy and could perform thumb opposition, but needle electromyography of the APB showed neurogenic changes and Type 4 (0.8%) had no thenar muscle atrophy, could perform thumb opposition, and needle electromyography showed no neurogenic changes. Over 10% of severe CTS patients have mild or no muscle atrophy and intact thumb opposition. The purpose of this study was to investigate the variations in thenar muscle innervation in patients with severe CTS.