The staggerer mouse carries a deletion in a gene encoding the nuclear hormone receptor RORalpha, which leads to severe impairments in phenotypic differentiation of cerebellar Purkinje cells. We previously found parasagittal compartments in the mature staggerer cerebellum, as defined by different transcription levels of Purkinje cell-specific molecules including calbindin. In the present study, we developed a hightiter anti-calbindin antibody to examine morphological features of the staggerer Purkinje cells. Immunohistochemistry for calbindin revealed compartmentalized Purkinje cell populations with different cell sizes, alignments, cell densities, and dendritic arborization, as well as different immunoreactivities, corresponding to the "transcriptional" compartments. Based on these immunohistochemical and cytological characteristics, the rostral cerebellum was clearly subdivided into three to seven parasagittal zones (Zones I-VII). Purkinje cells in Zones I and III were associated with the strongest calbindin immunoreactivities and exhibited morphological features reminiscent of the wild-type cells, i.e., large flask-shaped cell bodies, monolayer alignment, and arborized dendrites. Purkinje cells in Zone V were also labeled strongly, but they were small in cell size, ectopic and possessed long unbranched dendrites. On the other hand, Purkinje cells in Zones II, IV, and VI were very low in calbindin immunoreactivity and marked by small cell size, ectopia, poorly-developed dendrites and low cell density. Considering that this unique cytological compartmentalization emerges as the result of RORalpha gene mutation, it is suggested that normal cytodifferentiation of Purkinje cells is governed by both RORalpha-dependent and -independent mechanisms, and further that the latter mechanism might exert unevenly along the mediolateral cerebellar axis.