The cerebellum is a modular structure that integrates information in a topographical manner. The membrane receptors of the Eph family and their ligands play important roles in early regionalization, as well as in the formation of topographic connections of the nervous system. Here, we show that the expression of the Eph receptors -A4 and -A7, and of their ligands ephrin-A5 and -A2 correlates with the establishment of territories along the rostro-caudal axis and with the formation of topographically organized connections between the cortex and the cerebellar nuclei. While some sites where co-expression of receptors and ligands are evident, their relative expression mainly define sharp limits along the rostro-caudal axis and, at later stages, complementary gradients in the Purkinje cell layer and the deep cerebellar nuclei.