The regional mapping of reticulospinal, vestibulospinal, and vestibulo-ocular neuron groups onto specific axonal pathways was determined in the chicken embryo by retrograde axonal tracing. Experiments were performed on in vitro preparations of the brain stem to allow for precisely localized tracer injections combined with selective lesions of axon tracts. Brain-stem neuron groups were labelled from 3 days of embryonic development, when the first reticulospinal axons reached the cervical spinal cord, to 9 days of embryonic development, when each of the three systems studied had acquired a relatively mature organization. A striking feature at all stages was the spatial segregation of many neuron groups that projected along different trajectories. Examples of such segregation were found for neuron groups projecting in the same tract on different sides of the brain stem, in different tracts on the same side of the brain stem, and rostrally versus caudally. The occurrence of this segregation from early stages suggests that the choice of projection pathway by many brain-stem neurons is in some way linked to cell position. In some regions of the brain stem, neuron groups projecting along different pathways are intermingled. At least some of this intermingling, however, appears to occur subsequent to the initial establishment of axon projection patterns. Comparison of the mapping patterns at progressively older stages, and with previous mapping in the 11-day-old embryo (Glover and Petursdottir, 1988; Petursdottir, 1990) suggests that these projections are established with little error. The one obvious example of remodelling involved the pontine reticulospinal projection, in which an early contralateral axon population appeared to retract from spinal to medullary levels over the course of a few days. A similar phenomenon may be involved in the elimination of part of the contralateral reticulospinal projection from the midmedulla.