Although the overall topography of the cerebellar corticonuclear projection formed by Purkinje cell (PC) axons has been described, only a few studies have dealt with the organization of this projection at the level of individual PC axons. Thus, we reconstructed 65 single PC axons that were labeled with biotinylated dextran amine in the rat. We then analyzed the relationship between the projections of these PCs and the compartmentalization of the cerebellar cortex and nuclei based on the topography of olivocerebellar projection and aldolase C expression in PCs. After giving rise to short local recurrent collaterals near the soma, a PC axon formed a terminal arbor in a specific small area in the cerebellar nuclei (CN). The terminal arbors of vermal PCs were spread more widely than those of hemispheric PCs and sometimes extended to extracerebellar targets. PCs located in any of the aldolase C-positive (Groups I and II) and -negative (Groups III and IV) stripes consistently projected to the caudoventral and rostrodorsal parts of the CN, respectively, precisely in accordance with the compartmentalization of the cortex and nuclei. Mediolateral segregation and rostrocaudal convergence were seen between projections of separate PCs in a single aldolase C compartment. The results revealed a tight link between the projection patterns of individual PC axons, the topography of the olivocerebellar pathway, and the aldolase C expression pattern. Their overall correspondence seems to reflect a basic aspect of cerebellar organization, although some area-dependent variation in the relationship of these three entities was also present.