The parabrachial nucleus (PB) including the Kölliker-Fuse nucleus (KF) is considered to have an important role for the cortical and respiratory arousal from sleep. Recently, it has been reported that injection of Orexin-B, which is a hypothalamic neuropeptide responsible for the regulation of sleep-wakefulness, into the KF induces significant augmentation of the respiratory frequency and prolonged pre-inspiratory discharge of hypoglossal nerve. This implicates that orexinergic input to the KF may have a critical role for respiratory arousal. However, the synaptic organization between orexinergic fibers and KF neurons projecting to respiratory-related region is not fully elucidated. In the present study, we first examined orexinergic projections to the PB. After injection of cholera toxin B subunit (CTb) into the KF and immunostaining of orexin, a large number of CTb-labeled neurons was found in the tuberal hypothalamus, and 23% and 7% of them in the medial and perifornical parts and lateral part of the orexin field were revealed to be orexin-immunoreactive (ir), respectively. We further examined the overlap distribution of orexin-ir fibers and PB neurons projecting to the respiratory-related regions in the medulla oblongata and spinal cord by using retrograde-tracing and immunohistochemistry. Orexin-ir fibers were distributed mainly in the KF and lateral PB, and additionally in the medial PB. Neurons labeled with fluorogold (FG) injected into the ventrolateral medulla, phrenic nucleus, or hypoglossal nucleus were embedded in plexus of orexin-ir fibers in the KF. In these cases, orexin-ir axon terminals were seen frequently in close apposition to soma and dendrites of the KF neurons labeled with FG. Under an electron microscope, orexin-ir axon terminals made asymmetrical synaptic contacts with soma and dendrites of the FG-labeled neurons. These results suggest that orexinergic neurons are implicated in the respiratory arousal through their projections to the KF neurons that send their axons to the respiratory-related regions in the medulla oblongata and spinal cord.