The vertebrate brain is a remarkably complex anatomical structure which contains diverse subdivisions and neuronal subtypes with specific synaptic connections that contribute to the complexity of its function. The neural tube (the primordial brain) has to be progressively regionalized by means of precise control of the spatial and temporal arrangement of an orchestrated cocktail of genes. These will regulate inter- and intracellular signals driving a proper molecular patterning and specification of the distinct brain subdivisions, and thus will generate the structural basis of complexity and cellular diversity which characterize the brain.The present revision focuses on the main molecules involved during early development of the vertebrate cerebellum, the most rostral and dorsal structure of the hindbrain. We will survey the literature related to the early molecular mechanisms arising from the isthmus to pattern the caudal midbrain and rostral hindbrain primordia. The isthmus retains morphogenetic properties to further refining these subdivisions. Once the patterning of the cerebellar anlage is established, further molecular events (coming from the ventricular side and the rhombic lip) will specify the diverse neural cell population and the fine-tuning of the stereotyped morphology and layers of the cerebellum.Finally, we will discuss the combination of molecular genetics (gene expression pattern maps) and modern neuroanatomy (based on immunohistochemistry and highly sensitive neuroimaging), which have led to an increased interest in describing the neurodevelopmental mechanisms underlying structural disorders and intellectual discapacities that we currently observe in congenital anomalies of the human cerebellum.