Isolated cases of partial agenesis of atlas were initially considered benign variations, without any clinical or pathological significance. However, there is increasing evidence that neurological symptoms may occur even after minor cervical trauma in subjects with defects in the posterior arch of the atlas. The present case study describes a rare case of median deficiency in the posterior arch of atlas vertebra. The knowledge of this benign variation is crucial as it may aid clinicians in correct management of subjects presenting with resolution of symptoms and avoid excessive investigations.