We investigated whether glucocorticoids (i.e. corticosterone (CORT) in rats) released during sleep deprivation affect regional brain glycogen stores in 34-day-old Long-Evans rats. Adrenalectomized (with CORT replacement; ADX+) and intact animals were sleep-deprived for 6 h beginning at lights-on and then immediately sacrificed by microwave irradiation. Brain and liver glycogen and glucose, and plasma glucose levels were measured. After sleep deprivation (SD) in intact animals, glycogen levels decreased in the cerebellum and hippocampus, but not in the cortex or brainstem. By contrast, glycogen levels in the cortex of ADX+ rats increased by 43% (P<0.001) after SD, while other regions were unaffected. Also in ADX+ animals, glucose levels were decreased by an average of 28% throughout the brain after SD. Intact sleep-deprived rats had elevations of circulating CORT, blood and liver glucose that were absent in intact control and ADX+ animals. Different responses between brain structures after SD may be due to regional variability in metabolic rate or glycogen metabolism. Our findings suggest that the elevated glucocorticoid secretion during SD causes brain glycogenolysis in response to energy demands.