The elusive nature of dreams has intrigued philosophers and scientists since the birth of human kind. Compared to waking consciousness, dreaming defies many concepts of our ordinary reality, which has prompted many scholars to formulate several theories about its origin, meaning and functions. Despite the existence of a thorough analysis of dream content from western and non-western civilizations and several attempts concerning its interpretation and links with our waking life, it has remained impossible to identify the physical origin of dreams to date. Recent years have seen considerable progress in the development of sophisticated neuroimaging methods (high-density EEG, fMRI) allowing a stringent characterization of the brain mechanisms of a conscious state. Combining such techniques with reliable phenomenological methods such as serial awakenings during sleep, we have been able to describe the neural correlates of the dreaming experience and of specific dream content in healthy individuals and in patients with nightmares. These studies demonstrated that similar cortical networks are implicated for the same conscious content (e.g. perceptions, thoughts, emotions) across sleep and wakefulness in both healthy subjects and patients. We assume that the origins of a dream are located in subcortical regions of the brain and are related to the offline processing of motivational and emotional memory content during sleep. Combining EEG/MRI with serial awakenings represents a promising avenue for future developments in the science of dreaming, with the potential for decoding mental content from ongoing cortical and subcortical brain activity. Further studies showed that dreaming serves an emotion regulation function by exposing the individual to specific emotional stimuli, which would result in adapted responses to real-life events during wakefulness. By extrapolating this finding to clinical applications, we can propose new sleep therapies, which will aim to potentiate the emotional function of sleep and dreaming in order to treat several psychiatric disorders.