Mutations in the gene unc-53 of Caenorhabditis elegans result in behavioral and anatomical abnormalities. Immunocytochemistry and electron microscopy revealed neuroanatomical defects in all main longitudinal nervous tracts. Whole tracts were found to be misguided in specific ways suggesting that unc-53 affects pioneering axons. The four lateral microtubule cells (LMs), which are probably pioneering neurons, were examined in greatest detail. In the mutants, the processes of the LMs leave their normal position on the body wall and terminate prematurely. Examination of five unc-53 alleles for penetrance and expressivity of these defects revealed a spatial restriction in the requirement for unc-53. The morphology and positioning of the branch of the posterior lateral microtubule cells (PLMs) were also examined. In wild-type animals, the PLM branches lack the ultrastructural specializations of the main process, which include large microtubules, apposition to the cuticle, and a polarized extracellular matrix (the mantle). Two differences were noted in unc-53 mutants. First, a majority of PLMs branch at random and display an abnormally enlarged branching point and branch cross section. The unusual branch morphologies correlate with branch position, rather than PLM length. Second, the ectopic branches display the specific ultrastructural features characteristic of the main process. Furthermore, after entering the ventral nerve cord, the abnormal branches constantly change position relative to the other processes and the hypodermis, retaining their specialized microtubules throughout, but displaying a mantle only when in direct contact with hypodermis. Taken together, these observations suggest that the differentiated features of the PLMs, including process length, branch position, intracellular branch morphology, and surrounding extracellular matrix, are locally specified by cell-extrinsic cues, some of which require unc-53.