Brainstem nuclei such as the medullary reticular formation, raphe nuclei, pontine nuclei, locus coeruleus and subcoeruleus, among others, play a crucial role in arousal and sleep. Despite their involvement in critical functions, their study in living humans is challenging due to limited resolution and contrast of conventional MRI. First, we precisely delineated nine arousal/sleep brainstem nuclei in 7 Tesla MRI of healthy humans and generated their validated in-vivo stereotaxic probabilistic atlas. Second, we evaluated their structural connectivity using 7 Tesla High-Angular-Resolution-Diffusion-Imaging and probabilistic tractography. This atlas and connectome might help evaluating disorders of consciousness, sleep disorders and neurological disorders.