Atlanto-occipital assimilation is one of the most common congenital anomalies of the craniovertebral junction, and it usually is asymptomatic. We report a case of this malformation with unusual neurological symptoms which correlate with radiological findings. The anomaly caused the so-called foramen magnum syndrome, which was difficult to localize with neurological examination. The patient also had atlanto-axial dislocation, which was thought to enhance the symptoms with change of head/neck position.