Sleep is regulated by homeostatic mechanisms, and the low-frequency power in the electroencephalogram (delta power) during nonrapid eye movement sleep reflects homeostatic sleep need. Additionally, sleep is limited by circadian and environmentally influenced arousal. Little is known, however, about the underlying neural substrates for sleep homeostasis and arousal and about the potential link between them. Here, we subjected C57BL/6 mice to 6 h of sleep deprivation using two different methods: gentle handling and continual cage change. Both groups were deprived of sleep to a similar extent (>99%), and, as expected, the delta power increase during recovery sleep was quantitatively similar in both groups. However, in a multiple sleep latency test, the cage change group showed significantly longer sleep latencies than the gentle handling group, indicating that the cage change group had a higher level of arousal despite the similar sleep loss. To investigate the possible biochemical correlates of these behavioral changes, we screened for arousal-related and sleep needrelated phosphoprotein markers from the diencephalon. We found that the abundance of highly phosphorylated forms of dynamin 1, a presynaptic neuronal protein, was associated with sleep latency in the multiple sleep latency test. In contrast, the abundance of highly phosphorylated forms of N-myc downstream regulated gene 2, a glial protein, was increased in parallel with delta power. The changes of these protein species disappeared after 2 h of recovery sleep. These results suggest that homeostatic sleep need and arousal can be dissociated behaviorally and biochemically and that phosphorylated N-myc downstream regulated gene 2 and dynamin 1 may serve as markers of homeostatic sleep need and arousal, respectively. phosphoproteomics | two-dimensional difference gel electrophoresis S leep-wakefulness is continuously regulated by circadian and homeostatic mechanisms. In addition, multiple factors affect the level of arousal, including emotional, environmental, and physiological influences (1). During non-rapid eye movement (NREM) sleep, the homeostatic sleep need is correlated with the power in the delta wave band (i.e., 1-4 Hz) in the electroencephalogram (EEG). Delta power is augmented in proportion to previous wakefulness time and is dissipated during sleep. These findings imply that homeostatic sleep need is regulated by the durations of prior sleep and wakefulness (2). On the other hand, the level of arousal is inversely related to the likelihood of falling asleep and can be measured in terms of the sleep latency in the multiple sleep latency test (MSLT) (3). Because prolonged waking increases sleep need in addition to lowering the level of arousal, sleep latency often varies inversely with EEG delta power expressed during sleep (3). However, the level of arousal can be affected independently of time spent awake (for example, with stressful or exciting experiences during waking), implying that, under conditions of identical sleep deprivation time, the s...