The method described here outlines a simple protocol to investigate the in vivo function of axon guidance molecules during the development of the embryonic zebrafish brain. By 24 hours postfertilization, a simple scaffold of axon tracts and commissures can be visualised in the brain using acetylated alpha-tubulin, a panaxonal marker that stains all axons. The highly stereotypical trajectory of axons in the embryonic zebrafish brain provides an ideal system in which to study the molecular mechanisms of axon guidance, as defects in the axon scaffold can be clearly visualised. We describe here our approach to identify defects in the trajectory of axons that establish the initial template of tracts in the embryonic fore- and mid-brain. By combining immunohistochemical techniques and confocal microscopy on dissected wholemounts of embryonic brains we are able to observe at high resolution the complete scaffold of axon tracts. This approach provides a rapid and simple means of assessing axon guidance defects in the developing brain. Given the advantages of the zebrafish as a model system, and the range of molecular perturbation methods now available, this technique provides a valuable tool for assessing the phenotypic effects of gene perturbations in a biologically relevant context.