Naturally occurring neuronal death (NOND) is an essential phenomenon during the course of normal development of the nervous system. Studies in vivo and on organotypic cultures have helped to elucidate the basic histological and ultrastructural features, as well as the main cellular mechanisms of NOND in several areas of the brain. This review examines the existing evidence about the two waves of apoptotic cell death that affect the different types of cerebellar neurons in normal development and certain pathological conditions. The first wave regards neuronal progenitors and pre-migratory neuroblasts, the second post-migratory neuroblasts and mature neurons. The underlying cellular and molecular mechanisms are discussed critically also in the light of their relevance to neurodegenerative diseases.