The expression of innate reproductive, defensive, and ingestive behaviors appears to be controlled by three sets of medial hypothalamic nuclei, which are modulated by cognitive influences from the cerebral hemispheres, including especially the amygdala and hippocampal formation. PHAL analysis of the rat amygdala indicates that a majority of its cell groups project topographically (a) to hypothalamic behavior systems via direct inputs, and (b) to partly overlapping sets of hypothalamic behavior control systems through inputs to ventral hippocampal functional domains that in turn project to the medial hypothalamus directly, and by way of the lateral septal nucleus. Amygdalar cell groups are in a position to help bias or prioritize the temporal order of instinctive behavior expression controlled by the medial hypothalamus, and the memory of associated events that include an emotional or affective component.