The orexins are recently discovered neuropeptides that reportedly play a role in energy homeostasis, in addition to various other physiological processes. The synthesis of orexin A undergoes diurnal variation in certain areas of the brain, while the mutation of the orexin receptor 2 gene has been implicated in canine narcolepsy. Since the circadian pacemaker in the suprachiasmatic nucleus modulates the sleep/wake cycle, there is a putative role for orexins in the mammalian circadian system. In this study, immunohistochemical techniques were used to determine the distribution of orexin A in the structures of the hypothalamus and thalamus of Syrian and Siberian hamsters. In both species, the pattern of immunoreactivity was similar. Cells immunoreactive for orexin A were noted in the lateral hypothalamic area. Immunoreactive varicose orexin A fibres were found throughout the hypothalamus. The suprachiasmatic nucleus possessed little or no immunoreactive orexin A fibres in its core, but had fibres at its periphery. The thalamus of both species contained comparatively few immunoreactive fibres, which were mainly localised around the midline. The thalamic intergeniculate leaflet contained a plexus of immunoreactive orexin A fibres throughout its rostro-caudal extent. Three areas of the brainstem, the dorsal and median raphe nuclei and the locus coeruleus, were also investigated owing to their relevance to the circadian system and all were found to contain immunoreactive orexin A fibres. The presence of orexin A-immunoreactive fibres in the neural architecture of the mammalian circadian system suggests an important role for orexin A in circadian timekeeping processes.