The subparafascicular nucleus and the subparafascicular area are the major sites of synthesis of the recently discovered neuropeptide, tuberoinfundibular peptide of 39 residues (TIP39). Better knowledge of the neuronal inputs to the subparafascicular area and nucleus will facilitate investigation of the functions of TIP39. Thus, we have injected the retrograde tracer cholera toxin B subunit into the rostral, middle, and caudal parts of the rat subparafascicular nucleus. We report that the afferent projections to the subparafascicular nucleus and area include the medial prefrontal, insular, and ectorhinal cortex, the subiculum, the lateral septum, the anterior amygdaloid area, the medial amygdaloid nucleus, the caudal paralaminar area of the thalamus, the lateral preoptic area, the anterior, ventromedial, and posterior hypothalamic nuclei, the dorsal premamillary nucleus, the zona incerta and Forel's fields, the periaqueductal gray, the deep layers of the superior colliculus, cortical layers of the inferior colliculus, the cuneiform nucleus, the medial paralemniscal nucleus, and the parabrachial nuclei. Most of these regions project to all parts of the subparafascicular nucleus. However, the magnocellular subparafascicular neurons, which occupy the middle part of the subparafascicular nucleus, may not receive projections from the medial prefrontal and insular cortex, the medial amygdaloid nucleus, the lateral preoptic area, and the parabrachial nuclei. In addition, double labeling of cholera toxin B subunit and TIP39 revealed a remarkable similarity between input regions of the subparafascicular area and the brain TIP39 system. Neurons within regions that contain TIP39 cell bodies as well as regions that contain TIP39 fibers project to the subparafascicular area. Overall, the afferent connections of the subparafascicular nucleus and area suggest its involvement in central reproductive, visceral, nociceptive, and auditory regulation.