The Purkinje cells in the staggerer mutant mouse have various cellular abnormalities, including reduced cell number, ectopia, smaller size and absence of dendritic spines. It is also know that some of these abnormalities exhibit regional variations in the cerebellum. In this paper we have investigated expression in the staggerer Purkinje cells of the calbindin and inositol 1,4, 5-trisphosphate receptor type 1 mRNAs by in situ hybridization. Although the transcription levels of both mRNAs were significantly reduced compared with the wild-type cells, the reduction among the Purkinje cell populations was not even, varying greatly from region to region. Purkinje cells with different transcription levels were distributed in discrete regions and arranged alternately in the mediolateral direction. Moreover, the cell bodies with higher transcription levels were larger in size and aligned in a monolayer between the granular and molecular layers, whereas those with lower levels were smaller in size, fewer in number and dispersed throughout the granular layer. These findings suggest that there is a distinct mediolateral heterogeneity in the staggerer cerebellum with respect to transcription levels of these Purkinje cell-specific molecules, which might correlate with some cytological phenotypes.