Surgical treatment of craniocervical junction pathology has evolved considerably in recent years with the implementation of short fixation techniques rather than long occipito-cervical fixation (sub-axial). It is often difficult and sometimes misleading to determine the particular bone and vascular features (high riding vertebral artery, for instance) using only the conventional images in three orthogonal planes (axial, sagittal and coronal). The authors describe a rare clinical case of congenital malformation of the craniovertebral junction consisting of hypoplasia/agenesis of the odontoid process and bipartite atlas associated with atlantoaxial instability which was diagnosed late in life in a patient with a previous history of rheumatologic disease. The authors refer to the diagnostic process, including new imaging techniques, and three-dimensional multiplanar reconstruction. The authors also discuss the surgical technique and possible alternatives.