Cell migration is a crucial event for normal T cell development, and various ligand/receptor pairs have been indicated. Most of them, including chemokines and extracellular matrix proteins, have attractant properties upon thymocytes. Some other molecules can exert chemorepulsive effects, as we previously demonstrated for galectin-3. Nearly all these molecules are also expressed and can regulate the physiology of the nervous system. Conversely, some molecules initially described in the nervous system are also found in the immune system, notably in the thymus, suggesting their possible role as common mediators between neuroendocrine and immune systems. We summarize herein the data on the constitutive expression and role of typical neuron guiding molecules in the thymus. Furthermore, we discuss the complexity of thymocyte migration, which results from a network of molecular interactions, including those commonly found in the nervous system, and generate not only attraction, but also repulsion of migrating T cell precursors.