Studies in mammals have indicated a connection between circadian clocks and feeding behavior, but the nature of the interaction and its relationship to nutrient metabolism are not understood. In Drosophila, clock proteins are expressed in many metabolically important tissues but have not been linked to metabolic processes. Here we demonstrate that Drosophila feeding behavior displays a 24 hr circadian rhythm that is regulated by clocks in digestive/metabolic tissues. Flies lacking clocks in these tissues, in particular in the fat body, also display increased food consumption but have decreased levels of glycogen and a higher sensitivity to starvation. Interestingly, glycogen levels and starvation sensitivity are also affected by clocks in neuronal cells, but the effects of neuronal clocks generally oppose those of the fat body. We propose that the input of neuronal clocks and clocks in metabolic tissues is coordinated to provide effective energy homeostasis.