Programmed cell death (PCD) or apoptosis has crucial roles in the development of the nervous system and in tissue homeostasis. It is generally assumed that about half of the neurons are lost before completion of the neural architecture during development. Neurotrophic cell death in innervating neurons matches the number of neurons to the size of their target field. Damaged and potentially harmful cells are induced to apoptosis. The loss of developing neural cells is involved in the morphogenetic sculpting of the early nervous system and the creation of sexually dimorphic structures. PCD also eliminates pioneer neurons that serve transient functions, such as those that navigate in an environment devoid of other axons. Dysregulation of cell death programmes can feature in developmental and neoplastic disorders of the nervous system, including various neurodegenerative diseases. PCD is ultimately difficult process to measure because of their rapidly degradation by neighbors in a few hours or less. The molecular basis underlying why only certain cells are selected to die at adequate stage and how PCD is integrated with other biological processes are largely unknown. However, recent genetic studies in Drosophila and mice provide new insights into the regulatory system of cell death and survival pathway in vivo. This review describes the current knowledge about the significance and mechanisms of selective cell death in the nervous system.