The earliest step in establishing the complex neuronal networks in the vertebrate brain is the formation of a scaffold of axon tracts. How the formation of the early axon scaffold is controlled at the molecular level is unclear. Forming part of the scaffold, neurons located at the ventral midbrain-forebrain border (MFB) give rise to the medial longitudinal fascicle (mlf) and the posterior commissure (pc). We demonstrate that the homeobox genes Sax1, Six3, Emx2 and Pax6 are expressed in distinct domains in this area, suggesting that the specification of mlf and pc neurons might be controlled by the combinatorial activity of these transcription factors. We have tested this hypothesis by analysing the function of Sax1 in the embryonic chick brain. Gain-of-function experiments with Sax1 result in alterations to the early axon scaffold, most prominently an enlargement of the mlf at the expense of the pc. Ectopic expression of Sax1 also affects the expression of other ventral homeobox genes, particularly Six3 and Emx2. Our results indicate that the specification of neurons forming the early axon scaffold is governed by a homeobox code, thus resembling the mechanism of neuronal specification in the spinal cord.