Programmed cell death (PCD) or apoptosis is a phenomenon important for proper development and morphological as well as functional fine tuning of the nervous system. In the past two decades it became evident that the same apoptotic machinery, which has crucial functions in during development, can be reactivated under pathological circumstances in the adult nervous system and contribute to neuronal cell loss due to various neurological disorders like ischemic stroke, neurodegenerative diseases or brain traumata. In this review, we present the optic nerve transection paradigm as a valuable model for investigation of apoptotic neuronal cell death in the central nervous system (CNS). We review and summarize the most important discoveries regarding molecular pathways and mechanisms of neuronal apoptosis during the past few years, and outline contributions that have been made investigating the death of retinal ganglion cells (RGCs) following transection of the optic nerve.