Abstract Axonal projections from neurons located in the medial and lateral septal nuclei (MSN and LSN) were traced autoradiographically. The MSN projected bilaterally via a midline route to the diagonal band of Broca (DBB), the preoptic area (POA), the suprachiasmatic (SCN), paraventricular (PVN), ventromedial (VHM) and arcuate (ARC) nuclei including the median eminence (fiberous zone). Lateral coursing fibers traveled with the medial forebrain bundle (MFB) to the supraoptic (SON) and pre- and supra-mammillary nuclei. The majority of LSN axons projected to, and terminated in, the MSN. Fibers projected ipsilaterally through the POA, SON, SCN, ARC, ME and MMN with axonal projections observed throughout the MFB. In summary, the neurons of the MSN project to the medial hypothalamic nuclei via a midline route while LSN axons projected strongly to the MSN with the remaining ribers coursing along the ipsilateral MFB to terminate in several hypothalamic nuclei. These data indicate that a direct septo-hypothalamic pathway exists in the rat.