The development of the craniocervical junction is a complex sequence that requires perfect arrangement between cranial and cervical components. The neural crest cells of the upper somites and the notochord are both important in the development of this region. Of particular significance is the proatlas. Recent molecular studies have increased our knowledge of the processes involved in the formation of the base of the skull and upper cervical spine. The orchestration of the developing rhombencephalon and craniocervical junction is critical in the proper adult neuro-osseous relationships. Derailment of these processes may result in hindbrain herniation.