We have recently described a discrete region of the medullary raphe nuclei, termed the midline apneic site (MAS) that produces profound apnea upon chemical stimulation. The aim of the present study was to identify brain regions that innervate the MAS. The MAS was functionally identified and then the retrograde tracer, cholera toxin B subunit was injected in Sprague Dawley rats (n = 5). The MAS received projections of varying intensity from a number of brain regions previously associated with thermoregulation, fear, nociception, cardiovascular regulation and respiration. These include: the medial preoptic nucleus; median and lateral preoptic area; medial division of the bed nucleus of stria terminalis; paraventricular nucleus; central nucleus of the amygdala; dorsal hypothalamic area/dorsomedial hypothalamus; lateral hypothalamic area; lateral, ventrolateral and dorsomedial divisions of the periaqueductal grey; dorsal raphe nuclei; parabrachial nuclei; Kölliker-Fuse nucleus; intertrigeminal region; rostral ventrolateral medulla; lateral parafacial region; and the ventral respiratory group. The intermingling of functionally distinct cell groups in the raphe probably explains the large diversity of projections as found in other tracing studies of the raphe although the possibility remains that the MAS may integrate signals from multiple sites. The connection between the intertrigeminal region of the pons and the MAS indicates the possibility that this pathway participates in airway protective reflexes such as the Hering-Breuer and diving reflexes. One previously undescribed region that we have termed the lateral parafacial region was consistently labeled. The role of this region is yet to be determined.