Throughout the animal kingdom, the formation of the nervous system involves the elimination of many cells soon after their generation. This phenomenon, known as naturally occurring cell death, has precise time schedules and is observed in the vast majority of neural structures. It causes the loss of 15–85% of the neurons generated. Manipulations of the target structure can considerably affect the amount of cell death in a nervous center, but the regulation of this process is still controversial. While in some experiments cell death leads to a linear relationship between the size of the target and that of the input, other experiments show dramatic deviations from a linear prediction. It is quite possible that cell death is regulated by different mechanisms in different cases and that the search for a single explanation would be doomed to failure. However, it is shown here that if mutual trophic interactions are assumed to occur between connected structures, a general model can be developed for the regulation of histogenetic cell death in the developing nervous system of vertebrates. The model relies on few assumptions, all derived from a number of experimental studies. Cells destined to form a neural center are generated according to a program and die around a certain age unless a trophic factor is supplied that prevents their death. Target cells exert a trophic influence on input cells and vice versa. The model quantitatively describes the time course and the amount of cell death in neural structures, thereby reconciling in a unitary framework experimental findings that until now have appeared conflicting.