The cerebellum has long been known to play an important role in motor and balance control, and accumulating evidence has revealed that it is also involved in multiple cognitive functions. However, the evidence from neuroimaging studies and clinical observations is not well-integrated at the anatomical or molecular level. The goal of this review is to summarize and link different aspects of the cerebellum, including molecular patterning, functional topography images, and clinical cerebellar disorders. More specifically, we explored the potential relationships between the cerebrocerebellar connections and the expression of particular molecules and, in particular, zebrin stripe (a Purkinje cell-specific antibody molecular marker, which is a glycolytic enzyme expressed in cerebellar Purkinje cells). We hypothesized that the zebrin patterns contribute to cerebellar functional maps—especially when cerebrocerebellar circuit changes exist in cerebellar-related diseases. The zebrin stripe receives input from climbing fibers and project to different parts of the cerebral cortex through its cerebrocerebellar connection. Since zebrin-positive cerebellar Purkinje cells are resistant to excitotoxicity and cell injury while zebrin-negative zones are more prone to damage, we suggest that motor control dysfunction symptoms such as ataxia and dysmetria present earlier and are easier to observe than non-ataxia symptoms due to zebrin-negative cell damage by cerebrocerebellar connections. In summary, we emphasize that the molecular zebrin patterns provide the basis for a new viewpoint from which to investigate cerebellar functions and clinico-neuroanatomic correlations.