New insights into the physiopathological correlates of arousal and sleep fragmentation have recently been gained through experimental and clinical studies in healthy individuals and in patients with sleep disorders. The development of new analyses of autonomic system during sleep, has enriched the knowledge of sleep fragmentation derived from electroencephalographic analysis and has made possible the characterization of other phasic events arising from sleep, such as autonomic arousals. All of these studies provide evidence in support of the hypothesis that autonomic activations without cortical involvement are an epiphenomena of sleep fragmentation and altered sleep continuity, similar to that induced by cortical activation. This review begins by describing the latest findings on type of arousal response, with regards to the effect of arousing stimuli on the brain and the autonomic system. It then focuses on the hotly debated issue on experimental and clinical physiopathology of the arousals without cortical activation, highlighting the results of novel studies on the neural substrates mediating these response. Finally, we address the current question on clinical significance of sleep fragmentation to understand if arousal per se, cortical or autonomic, has an impact on daytime functioning, cardiovascular consequences and cognitive sequelae.