'atlanto-' originates from New Latin/Gk. anatomical usage based on the word 'atlas' (from Greek 'Ἄτλας'), where 'atlas' was used to name the first cervical vertebra that 'supports' the head; 'odontoid' originates from Greek 'odónt-' or 'odont-' meaning 'tooth' plus the suffix '-oid' meaning 'resembling' (so 'odontoid' = 'tooth-like').

'atlanto-odontoid' developed in modern anatomical English by combining the combining form 'atlanto-' (from 'atlas') and the Neo-Latin/Greek-derived 'odontoid' (from 'odont- + -oid'); similar compound forms appeared in New Latin and 19th–20th century anatomical literature and eventually standardized in modern English as 'atlanto-odontoid'.

Initially it named the anatomical relationship of the atlas and the tooth-like odontoid process; this core meaning has remained stable, now used both descriptively (adjective) and as a noun for the joint or region.