Association between sleep disturbances and hormonal imbalances can result in metabolic disorders, including obesity and diabetes. The hypothalamus is likely to play a part in these pathophysiological conditions because it contains sleep-wake circuits that are sensitive to metabolic hormones, including leptin and ghrelin. Thus, shared hypothalamic circuits such as the hypocretin and melanin-concentrating hormone systems are strong candidates for mediating both sleep and metabolic imbalances. This review reveals new roles for these systems as sensors and effectors of sleep and wakefulness, and discusses their plasticity in regulating sleep and energy balance. New optical tools that remotely control neuronal circuit activity provide an effective means to understand the cooperativity of shared circuits in regulating hypothalamic functions such as sleep and metabolism.