The atlanto-occipital joint (AOJ) is an important transitional region, which supports and stabilizes the cranium to the spine with its surrounding ligamentous structures. An injury to this joint is often accompanied by brain injury and may be fatal. A good understanding of the anatomy of this joint is required to timely diagnose an AOJ instability and intervene via the means of an immediate fixation. We discuss the normal anatomy of and anatomical variations within the occipito-atlantoaxial complex, the classification systems to describe its disruption, and its clinical significance.