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Early axon tracts in the developing vertebrate brain are established along precise paths. Yet, little is known about axon guidance processes at early stages of rostral brain development. Using whole mount in situ hybridisation in combination with immunohistochemistry, we have analysed the expression patterns of Slits, Netrins, Semaphorins and the respective receptors during the formation of the early axon scaffold, particularly focusing on the pretectal-mesencephalic boundary. Many of these guidance molecules are expressed in close correlation with the growing tracts, and the nuclei of the corresponding neurons often express the respective receptors. The expression patterns of Slits and Netrins implicate them with the positioning of the longitudinal tracts along the dorsoventral axis, while Semaphorins could provide guidance at specific choice points. Our study provides a catalogue of gene expression for future studies on axon guidance mechanisms in the early brain.