Afferent fibers from the amygdala to subdivisions of lateral, ventromedial and dorsomedial hypothalamic nuclei were investigated in rat by retrograde transport of horseradish peroxidase. Small (intranuclear size) peroxidase deposits were placed in hypothalamic nuclei by iontophoresis of a tracer solution containing poly-L-alpha-ornithine which greatly limited diffusion. The medial, central and amygdalo-hippocampal nuclei of the amygdala were found to be the major donors of amygdaloid afferent fibers to the hypothalamus, but there was also substantial labeling of somata in cortical, basomedial, basolateral and lateral amygdaloid nuclei and the intra-amygdaloid bed nucleus of the stria terminalis. No fibers projected from the posterior cortical nucleus of the amygdala to the hypothalamus. Most amygdaloid projections to the lateral hypothalamic area originated in the anterior half of the amygdala, while projections to the ventromedial hypothalamic nucleus arose along the entire length of the amygdala except the posterior cortical nucleus. The amygdalo-hippocampal area projects to the medial hypothalamus. Other amygdaloid nuclei project to both the medial and lateral hypothalamic nuclei. These topographic organizations of amygdaloid afferent fibers to various subdivisions of the hypothalamic nuclei are discussed and compared with other anatomical studies on these connections.