The role of specific axonal tracts for the guidance of growth cones was investigated by examining axonal outgrowth within the abnormal brain tracts of zebrafish cyclops mutants. Normally, the earliest differentiating neurons in the zebrafish brain establish a simple scaffold of axonal tracts. Later-developing axons follow cell-specific pathways within this axonal scaffold. In cyclops embryos, this scaffold is perturbed due to the deletion of some ventromedial neurons that establish parts of the axonal scaffold and the development of an abnormal crease in the brain. In these mutant embryos, the growth cones projected by the neurons of the nucleus of the posterior commissure (nuc PC) are deprived of the two tracts of axons that they sequentially follow to first extend ventrally, then posteriorly. These growth cones respond to the abnormal scaffold in several interesting ways. First, nuc PC growth cones initially always extend ventrally as in wild-type embryos. This suggests that for the first portion of their pathway the axons they normally follow are not required for proper navigation. Second, approximately half of the nuc PC growth cones follow aberrant longitudinal pathways after the first portion of their pathway. This suggests that for the longitudinal portion of the pathway, specific growth cone/axon interactions are important for guiding growth cones. Third, although approximately half of the nuc PC growth cones follow aberrant longitudinal pathways, the rest follow normal pathways despite the absence of the axons that they normally follow. This suggests that cues independent of these axons may be capable of guiding nuc PC growth cones as well. These results suggest that different guidance cues or combinations of cues guide specific growth cones along different portions of their pathway.