Anatomical studies and stimulation studies in the decerebrate animal have suggested that the muscle atonia of rapid eye movement (REM) sleep is mediated by a projection from cholinoceptive glutamatergic neurons in the pons to the nucleus magnocellularis (NMC) of medulla. This model suggests that glutamate release in NMC should be enhanced in REM sleep. In the present study, glutamate release across the sleep-wake cycle in NMC was measured by in vivo microdialysis. We found that glutamate release in NMC was significantly higher (p = 0.0252) during REM sleep than during wakefulness (W). Glutamate release during REM sleep was not elevated either in nucleus paramedianus (NPM) or in the pontine inhibitory area (PIA) regions where cholinergic stimulation suppresses muscle tone. Acetylcholine (ACh) microinjection into PIA enhanced glutamate release in NMC. These results support the hypothesis that a glutamatergic pathway from PIA to NMC is responsible for the suppression of muscle tone in REM sleep.