The organization of hypothalamic projections to the cerebral cortex in the rat has been studied using retrograde and anterograde tracer methods. Four separate populations of hypothalamic neurons, which constitute a major source of diffuse cortical innervation, were identified: Tuberal lateral hypothalamic (LHAt) neurons which innervate the cerebral cortex tend to cluster in the perifornical region, in the zona incerta, and along the medial edge of the cerebral peduncle, at levels roughly coextensive with the ventromedial hypothalamic nucleus. Most of these neurons project to the ipsilateral cortex; a small percentage innervate the contralateral cortex, but this varies among cortical terminal fields. The perifornical neurons are organized in a roughly topographic medial-to-lateral relationship with respect to their cortical terminal fields. Field of Forel (FF) neurons, which project primarily to the frontal cortex of the ipsilateral hemisphere, are located just ventral to the medial edge of the medial lemniscus, at the level of the ventromedial basal thalamic nucleus. The more laterally placed neurons innervate the lateral frontal, insular and perirhinal cortex; the more medial neurons, around the mammillothalamic tract, innervate the medial frontopolar, prelimbic, infralimbic, and anterior cingulate cortex. Posterior lateral hypothalamic (LHAp) neurons form a dense cluster spanning the lateral hypothalamus, from the cerebral peduncle to the posterior hypothalamic area at premammillary levels, and extending into the supramammillary nucleus and the adjacent ventral tegmental area. LHAp neurons innervate the entire cerebral cortex, predominantly on the ipsilateral side. Populations of LHAp neurons projecting to different cortical target areas show considerable spatial overlap, but computer plots of the centers of these populations demonstrate a strict topographic relationship with respect to the cerebral cortex. Tuberomammillary (TMN) neurons form a sheet along the ventrolateral surface of the premammillary hypothalamus. About twice as many TMN neurons innervate the ipsilateral, as compared to the contralateral hemisphere; it is not known whether single neurons project to both hemispheres. No topographic organization of the TMN cortical projection is apparent. Injections of different-colored fluorescent dyes into various cortical areas demonstrate that hypothalamic neurons in general have rather restricted cortical terminal fields. Only occasional neurons are found, primarily in LHAt, which are double labeled by injections into different cytoarchitectonic areas.(ABSTRACT TRUNCATED AT 400 WORDS)