The suprachiasmatic nucleus (SCN) of the hypothalamus houses the main mammalian circadian clock. This clock is reset by light-dark cues and stimuli that evoke arousal. Photic information is relayed directly to the SCN via the retinohypothalamic tract (RHT) and indirectly via the geniculohypothalamic tract, which originates from retinally innervated cells of the thalamic intergeniculate leaflet (IGL). In addition, pathways from the dorsal and median raphe (DR and MR) convey arousal state information to the IGL and SCN, respectively. The SCN regulates many physiological events in the body via a network of efferent connections to areas of the brain such as the habenula (Hb) in the epithalamus, subparaventricular zone (SPVZ) of the hypothalamus and locus coeruleus of the brainstem-areas of the brain associated with arousal and behavioral activation. Substance P (SP) and the neurokinin-1 (NK-1) receptor are present in the rat SCN and IGL, and SP acting via the NK-1 receptor alters SCN neuronal activity and resets the circadian clock in this species. However, the distribution and role of SP and NK-1 in the circadian system of other rodent species are largely unknown. Here we use immunohistochemical techniques to map the novel distribution of SP and NK-1 in the hypothalamus, thalamus and brainstem of the Alaskan northern red-backed vole, Clethrionomys rutilus, a species of rodent currently being used in circadian biology research. Interestingly, the pattern of immunoreactivity for SP in the red-backed vole SCN was very different from that seen in many other nocturnal and diurnal rodents.