The transcriptional regulator Pax6 is expressed in cerebellar granule cells and a mutation in that gene (Sey) has been shown to affect cerebellar development. We have defined novel phenotypes in the Sey/Sey cerebellum, indicating that the mutation of Pax6 alters granule cell behavior in vitro and also the interaction between granule cells and Purkinje cells in vivo. In culture, Sey/Sey granule cell precursors show the following abnormal phenotypes: enhanced proliferation, increased apoptotic cell death, and decreased number of morphologically differentiating beta-III tubulin-positive cells. There is an overlap in the populations of Sey/Sey cells that express markers for proliferation and neuronal differentiation indicating an abnormality in the transition between these states in granule cells. In vivo, Purkinje cell ectopias were found deep in the cerebellum and extending into the inferior colliculus. Coincident with this, Purkinje cell phenotype was the alteration in the pattern and levels of Reelin expression in granule cells of the external germinal layer (EGL). The finding of increased staining for Disabled-1, a signaling pathway intermediary that is normally downregulated by a Reelin signal, throughout the Purkinje cell population suggests that in the Sey/Sey cerebellum there is a disruption in Reelin signaling from the EGL to Purkinje cells. These findings suggest that Pax6 is critical for the proper differentiation of granule cells and their communication with developing Purkinje cells. Thus, through its guidance of granule cell development, Pax6 also has a strong influence on many of the cellular programs that guide the morphogenesis of the entire cerebellum.