We developed a rapid method that uses diphtheria toxin, the flp recognition target sequences, and the GAL4-UAS activation system, to ablate specific neurons in the Drosophila embryo and to examine the consequences in large numbers of embryos at many time points. We used this method to show that, in the absence of the aCC axon, which pioneers the intersegmental nerve in the PNS, the three U follower axons are delayed and make frequent errors. However, the pathway ultimately forms in most segments. We also ablated the axons that pioneer the first longitudinal pathways within the CNS and observed similar results; the formation of longitudinal pathways is delayed and disorganized in 70% of segments, but these tracts ultimately form in 80% of segments. Thus, pioneers facilitate the development of PNS and CNS axon pathways; in their absence, followers are delayed and make numerous errors. However, pioneers are not absolutely required, as these embryos display a remarkable ability to correct for the loss of the pioneering neurons.