The efferent connections of the medial (MHb) and lateral (LHb) habenular nuclei in the rat were demonstrated autoradiographically following small injections of tritiated amino acids localized within various parts of the habenular complex. Comparison of individual cases led to the following conclusions. MHb efferents form the core portion of the fasciculus retroflexus and pass to the interpeduncular nucleus (IP) in which they terminate in a topographic pattern that refects 90 degrees rotations such that dorsal MHb projects to lateral IP, medial MHb to ventral, and lateral MHb to dorsal IP. Most MHb fibers cross in the interpeduncular necleus in the "figure 8" pattern described by Cajal, and terminate throughout the width of IP with only moderate preference for the ipsilateral side. However, the most dorsal part of MHb projects almost exclusively to the most lateral IP zone in a cluster pattern that is particularly dense on the ipsilateral side. The MHb appears to have no other significant projections, but very sparse MHb fibers may pass to the supracommissural septum and to the median raphe nucleus. Except for some fibers passing ventrally into the mediodorsal nucleus, all of the LHb efferents enter the fasciculus retroflexus and compose the mantle portion of the bundle. No LHb projections follow the stria medullaris. In the ventral tegmental area LHb efferents become organized into groups that disperse in several directions: (a) Rostrally directed fibers follow the medial forebrain bundle to the lateral, posterior and dorsomedial hypothalamic nuclei, ventromedial thalamic nucleus, lateral preoptic area, substantia innominata and ventrolateral septum. (b) Fibers turning laterally distribute to the substantia nigra, pars compacta (SNC); a small number continue through SNC to adjacent tegmentum. (c) The largest contingent of LHb efferents passes dorsocaudally into paramedian midbrain regions including median and dorsal raphe nuclei, and to adjacent tegmental reticular formation. Sparse addition LHb projections pass to the pretectal area, superior colliculus, nucleus reticularis tegmenti pontis, parabrachial nuclei and locus coeruleus. No LHb projections appear to involve the interpeduncular nucleus. All of these connections are in varying degree bilateral, with decussations in the supramammillary region, ventral tegmental area and median raphe nucleus. On the basis of differential afferent and efferent connections, the LHb can be divided into a medial (M-LHb) and a lateral (L-LHb) portion. The M-LHb, receiving most of its afferents from limbic regions and only few from globus pallidus, projects mainly to the raphe nuclei, while L-LHb, afferented mainly by globus pallidus and in lesser degree by the limbic forebrain, projects predominantly to a large region of reticular formation alongside the median raphe nucleus. Both M-LHb and L-LHb, however, project to SNC. The reported data are discussed in correlation with recent histochemical findings.