The physiological role and relevance of the mechanisms sustaining circadian rhythms have been acknowledged. Abnormalities of the circadian and/or sleep-wakefulness cycles can result in major metabolic disorders or behavioral/professional inadequacies and stand as independent risk factors for metabolic, psychiatric, and cerebrovascular disorders and early markers of disease. Neuroimaging and clinical evidence have documented functional interactions between autonomic (ANS) and CNS structures that are described by a concept model (Central Autonomic Network) based on the brain-heart two-way interplay. The circadian rhythms of autonomic function, ANS-mediated processes, and ANS/CNS interaction appear to be sources of variability adding to a variety of environmental factors, and may become crucial when considering the ANS major role in internal environment constancy and adaptation that are fundamental to homeostasis. The CNS/ANS interaction has not yet obtained full attention and systematic investigation remains overdue.