This is the first study of the prenatal development of septal projections to the hypothalamus in rats, using carbocyanine dyes (DiI and DiA) as retrograde tracers. First septal neurons send axons to the preoptic area and anterior hypothalamus on embryonic day 14,5 (E14,5) and on E15 numerous labeled neurons are visualized in the septum after DiI insertion into the preoptic region. On E18 and E20 these neurons develop numerous spiny dendrites that occupy all rostrocaudal extension of the septum with concentration in the ventral part of the septum. Only a few septal neurons send their axons to the mediobasal hypothalamus at E15 confirmed by double-labeling (DiI+DiA) experiments on E20-E21. All septo-hypothalamic connections are unilateral and the number of the neurons revealed in the septum correlates with the place and size of the DiI insertion in the hypothalamus: more lateral and anterior hypothalamic marker insertions always resulted in significant neuronal labeling in the septum. No septal connections with the posterior hypothalamus specifically, the mammillary bodies are formed prenatally. We have demonstrated that the development of septal projections to various rostrocaudal regions of the hypothalamus take place during different stages of development. Prominent parts of the septal projections are to the preoptic area and anterior hypothalamus while few connections with the mediobasal hypothalamus are formed prenatally. These data provide basic knowledge of early steps of the development of the septo-hypothalamic connections.