The central nucleus of the amygdala (CeA) is generally regarded as a control nucleus of subcortical target systems. Due to its widespread projections to different brain areas it is able to modulate emotional behavior of the organism. However, it is still not clear whether single neurons of the CeA project to different areas or to one target area. Injections of the retrograde tracers Fluorogold and True Blue into target regions of the central nucleus of the amygdala, i.e., the substantia innominata (SI) and the caudal pontine reticular nucleus (PNC), revealed overlapping but otherwise distinct neuronal populations within mainly the medial division of the CeA. From our study we conclude that SI and PNC receive input from different subsets of amygdala neurons.