The suprachiasmatic nucleus (SCN) is a dominant pacemaker involved in the generation of circadian rhythms in mammals. Surprisingly, the expression of the many rhythms appears to be mediated via a limited efferent projection system of the pacemaker, of which the largest pathway terminates in the subparaventricular area and in the paraventricular nucleus of the hypothalamus. In order to investigate a possible topographical organization of this major outflow pathway of the SCN, microiontophoretic injections of the anterograde tracer Phaseolus vulgaris-leucoagglutinin (PHA-L) or the retrograde tracer cholera toxin subunit B (ChB) were centered in distinct subparts of the SCN (PHA-L) or in the subparaventricular area-paraventricular nucleus (ChB), respectively. PHA-L injections involving the entire SCN revealed not only a major projection to the subparaventricular area, but also one directed towards the medial and dorsal parvicellular subnuclei of the paraventricular nucleus. As opposed to injections involving the entire nucleus, injections of PHA-L centered in the dorsomedial subdivision of the SCN resulted in a relatively larger number of PHA-L-immunoreactive fibers in the parvicellular subdivisions of the PVN, whereas the terminal field in the subparaventricular area was less substantial. A topography of the SCN efferent output system was also revealed by the retrograde tracing with ChB. Injections of ChB in the dorsal part of the paraventricular hypothalamic nucleus, not involving the underlying subparaventricular area, gave rise to a population of retrogradely labeled cells in the dorsomedial part of the SCN. In contrast, ChB injections in the subparaventricular area resulted in labeling of neurons clustered in a more ventrolateral aspect of the SCN. The present data provide evidence for a topography in the major efferent projection system from the SCN, implying that different subparts of the rat SCN, presumably containing partly different potential neurotransmitter substances, may regulate different circadian rhythms.