The hippocampal formation and amygdala are responsible for regulating emotion, learning, and behavior. The hippocampal projection to the amygdala has been demonstrated to originate in the subiculum and adjacent portion of field CA1 of the Ammon's horn (Sub/CA1) in the rat; however, the topographical organization of this pathway is still understudied. To make it clear, we performed anterograde and retrograde tracing with biotinylated dextran amine (BDA) and cholera toxin B subunit (CTb), respectively, in the rat. A series of BDA experiments revealed that the temporal-to-septal axis of origin determined a medial-to-lateral axis of termination in the amygdala. Briefly, the temporal region of the Sub/CA1 projects preferentially to the medial amygdaloid region including the medial, intercalated, and basomedial nuclei and the amygdalohippocampal transition area, and progressively more septal portions of the Sub/CA1 distribute their efferents in more lateral regions of the amygdala. Sub/CA1 fibers distributed in the central amygdaloid nucleus were relatively few. Retrograde tracing with CTb confirmed this topography and revealed little hippocampal innervation of the central nucleus of the amygdala. These observations suggest that distinct Sub/CA1 regions arranged along the longitudinal hippocampal axis may influence distinct modalities of the amygdala function. J. Comp. Neurol. 496:349–368, 2006. © 2006 Wiley-Liss, Inc.