Recent discoveries on the way in which the cerebellum carries out higher non-motor functions, have stimulated a proliferation of researches into functional integration and neural mechanisms in the cerebellum. Cerebellar functional asymmetry is a special characteristic of cerebellar functional organization and the cerebro-cerebellar circuitry that underlies task performance. Multi-level neuroimaging studies demonstrate that cerebellar functional asymmetry has a rather complex pattern, and may be correlated with practice or certain disorders. In this review, we summarize some new and important advances in the understanding of functional laterality of the cerebellum in primary motor and higher cognitive functions, and highlight the differences in the patterns of cerebellar functional asymmetry in the various functional domains. We propose that cerebellar functional asymmetry may be associated with the pattern of connectivity between a large number of widely distributed brain areas and between special cerebellar functional regions. It is suggested that cerebro-cerebellar circuits in particular play an important role in cerebellar functional asymmetry. Finally, we propose that multi-scale connectivity analyses and careful studies of high-level cerebellar functional asymmetry would make an important contribution to the understanding of the human cerebellum and cerebral neural networks.