Pax6, a paired homeobox DNA binding protein, has been found to be expressed in the cerebellum in both granule cells and their precursors in the external granular layer (EGL). In this study we have traced Pax6 expression through embryonic development in mice by using a polyclonal antibody against Pax6 and used it to study the cellular dispersal pattern of the EGL. During dispersal the EGL was thicker and Pax6 expression was more intense on the rostral side of the lateral corners of the cerebellum. Pax6 immunoreactive cells were found to be migrating from the EGL during the early stage of EGL dispersal, which suggested the early inward migration of granule cells. Double staining with various markers confirmed that the early-migrating cells are not Purkinje cells, interneurons or glia. Although the Pax6 immunoreactive cells within the cerebellum were not apparently proliferating, NeuN, a marker for postmitotic granule cells, was not expressed in these cells until E16. Furthermore, granule cells were observed migrating inwards from the EGL both during and after EGL dispersal. These early migrating granule cells populated the whole cerebellum. These findings offer novel views on specific stages of granule cell dispersal and migration.