A 14-year-old Japanese boy presented with myelopathy due to atlas hypoplasia with complete posterior arch. Decompressive laminectomy of the atlas produced good neurological recovery, and follow-up T2-weighted magnetic resonance imaging showed disappearance of spinal cord edema. Congenital atlas stenosis may be symptomatic even in children, with no accompanying cervical spondylotic change. Such cases have previously occurred only in Asian adults. A radiological study of the patient's brother showed median cleft formation of the posterior arch of atlas, indicative of a wide spectrum of atlas anomalies and a possible genetic relationship between these anomalies.