Atlanto-occipital assimilation is a congenital craniovertebral junction malformation where the partial or complete fusion of the atlas and occiput occurs. Atlanto-occipital assimilation can be associated with numerous complications, including basilar invagination, atlantoaxial subluxation, Chiari malformation, congenital vertebral bodies fusion, and cord compression. As a result, vigilant identification and accurate reporting of atlanto-occipital assimilation are essential. The purpose of this review article is to discuss the numerous complications and associations of atlanto-occipital assimilation, such that an accurate diagnosis could be made for this commonly missed pathology.