Sleep has been functionally implicated in brain energy homeostasis in that it could serve to replenish brain energy stores that become depleted while awake. Sleep deprivation (SD) should therefore lower brain glycogen content. We tested this hypothesis by sleep depriving mice of three inbred strains; i.e., AKR/J (AK), DBA/2J (D2), and C57BL/6J (B6) which differ greatly in their sleep regulation. After a 6-h SD, these mice and their controls were sacrificed by microwave irradiation and glycogen and glucose were quantified in the cerebral cortex, brainstem, and cerebellum. After SD, both measures significantly increased by ~40% in the cortex of B6 mice while glycogen significantly decreased by 20-38% in brainstem and cerebellum of AK and D2 mice. In contrast, after SD, glucose content increased in all three structures in AK mice and did not change in D2 mice. The increase in glycogen after SD in B6 mice persisted under conditions of food deprivation that, by itself, lowered cortical glycogen. Furthermore, the strains that differ most in their compensatory response to sleep loss, i.e., AK and D2, did not differ in their glycogen response. Thus, glycogen content per se is an unlikely end-point of sleep's functional role in brain energy homeostasis.