Respiration shares strong functional links with the brain, influencing perception, emotions and cognition. In turn respiration is modulated by sensory stimuli, attention and vigilance states. To explore this intricate brain-body relationship, we performed intranasal pressure recordings in freely-moving mice paired with extracellular recordings in the CA1 region of the hippocampus to precisely detect Wake, non-REM and REM sleep epochs. We characterized different respiratory cycle features between vigilance states and uncovered unexpected breathing dynamics at transitions between them. To show how strong and general across animals these links are, we trained an artificial neuronal network with respiratory features only and demonstrated reliable prediction of brain states. Next, we focused on the fine architecture of respiration during Wake. Examination of individual respiratory cycles revealed the presence of respiratory “pauses” intermingled between inhalation and exhalation and characterized by a flat pressure signal (i.e. no airflow). Pauses vary independently of inhalations and exhalations and their duration is crucial for dictating the respiration rate. With these premises, we questioned whether respiration modulates the activity of hippocampal and piriform cortices, brain regions sharing similar anatomical (archeocortices with 3 layers) and circuitry (recurrent connections) features. Using silicon-probe recordings coupled to nasal pressure monitoring, we found region-specific LFP modulations and a significant recruitment of units, especially at the transition between inhalation and pauses, and independently of cycle length. Altogether, these results show that specific events within respiratory cycles modulate activity in archeocortices, supporting the view of respiration acting as a widespread neural synchronizer throughout the brain.