The aim of the present study was to identify the specific afferent projections to the rostral and caudal nucleus raphe magnus, the gigantocellular reticular nucleus pars alpha and the rostral nucleus raphe pallidus. For this purpose, small iontophoretic injections of the sensitive retrograde tracer choleratoxin (subunit b) were made in each of these structures. In agreement with previous retrograde studies, after all injection sites, a substantial to large number of labeled neurons were observed in the dorsal hypothalamic area and dorsolateral and ventrolateral parts of the periaqueductal gray, and a small to moderate number were found in the lateral preoptic area, bed nucleus of the stria terminalis, paraventricular hypothalamic nucleus, central nucleus of the amygdala, lateral hypothalamic area, parafascicular area, parabrachial nuclei, subcoeruleus area and parvocellular reticular nucleus. In addition, depending on the nucleus injected, we observed a variable number of retrogradely labeled cells in other regions. After injections in the rostral nucleus raphe magnus, a large number of labeled cells were seen in the prelimbic.