Structure-function analyses of the mammalian brain have historically relied on anatomicallybased approaches. In these investigations, physical, chemical, or electrolytic lesions of anatomical structures are applied, and the resulting behavioral or physiological responses assayed. An alternative approach is to focus on the expression pattern of a molecule whose function has been characterized and then use genetic intersectional methods to optogenetically or chemogenetically manipulate distinct circuits. We previously identified WIDE AWAKE (WAKE) in Drosophila, a clock output molecule that mediates the temporal regulation of sleep onset and sleep maintenance. More recently, we have studied the mouse homolog, mWAKE/ANKFN1, and found that its role in the circadian regulation of arousal is conserved.Here, we perform a systematic analysis of the expression pattern of mWake mRNA, protein, and cells throughout the adult mouse brain. We find that mWAKE labels neurons in a restricted, but distributed manner, in multiple regions of the hypothalamus (including the suprachiasmatic nucleus), the limbic system, sensory processing nuclei, and additional specific brainstem, subcortical, and cortical areas. Interestingly, mWAKE is also observed in non-neuronal ependymal cells. In addition, to describe the molecular identities and clustering of mWake + cells, we provide detailed analyses of single cell RNA sequencing data from the hypothalamus, a region with particularly significant mWAKE expression. These findings lay the groundwork for future studies into the potential role of mWake + cells in the rhythmic control of diverse behaviors and physiological processes. manner across multiple regions of the mouse brain. These areas span the brainstem, subcortical areas, and cortex, with particularly prominent expression in the hypothalamus, and include not only mWake + neurons but also ependymal cells that line the cerebral ventricles. Although the precise functions of these mWake + regions remain to be determined, their locations are suggestive of potential roles in circadian-related behaviors, arousal, sensory processing, and emotion. These results comprise a catalog of mWake expression in the mouse brain and mWake + cell identity in the hypothalamus and may ultimately lead to the identification of neural circuits mediating the circadian regulation of arousal and other internal states and behaviors.