The functional neuroanatomy of vestibulo-ocular and vestibulospinal projections has been studied in the chicken embryo as a step towards elucidating the developmental mechanisms that determine the connectivity patterns of the vestibular system. Retrograde and anterograde axonal tracing, neurotransmitter immunohistochemistry, and retrograde transport of radiolabelled neurotransmitters or neurotransmitter analogs demonstrate that vestibular neurons are clustered into functionally specific populations. Each of these has a characteristic positional domain, projection pathway, and site of termination. At early embryonic stages, the positional domains of the various populations are systematically correlated with segmental and longitudinal territories of differential gene expression in the hindbrain. The intimate link between position and phenotype at these stages suggests that the functional identity of vestibular neurons is determined, at least in part, by mechanisms associated with early pattern formation of the neural tube.