Non-rapid eye movement (NREM) sleep is characterised by reduced consciousness; thus, studying its neural characteristics acts as a useful indication of what is needed for conscious experience. The integrated information theory (Tononi, 2008) states that the ability of different thalamocortical regions to interact is crucial for consciousness, thereby motivating research concerning connectivity changes in the thalamocortical system that accompany changing consciousness levels. This review aims to discuss investigations of functional connectivity of resting-state and large-scale brain networks, applying correlational approaches to neuroimaging data as well as studies that used brain stimulation to investigate effective connectivity. Most findings suggest a reorganisation of functional brain networks where inter-region connectivity is reduced and intra-region connectivity is stronger in deep sleep than wakefulness.