A 10-year-old boy with Klippel-Feil syndrome had progressive atrophy of the left thenar eminence and absence of left radial pulse. Neurophysiologic studies and angiography were normal. However, duplex sonography over the wrists revealed an aberrant left radial artery. We speculate that the thenar atrophy in this patient is congenital, which may be due to the anomaly of the left radial artery, and is further compromised by vascular compression in the thoracic outlet.