Interleukin-6 (IL-6) has been implicated in excessive daytime sleepiness (EDS) in humans, and exogenous IL-6 also induces sleep alterations both in humans and rats. The IL-6 levels in human blood vary with the light-dark cycle with IL-6 levels being high during the dark period and low during the light period, whereas in the pituitary of rats the IL-6 levels are elevated during the light period compared to the dark period. However, it is unknown whether IL-6 in the brain is affected by the light-dark cycle. We hypothesized that IL-6 levels in the brain are regulated by the light-dark cycles and are elevated during the period that is predominantly occupied by sleep. To test this hypothesis, we measured IL-6 levels in the brain, blood, and adipose tissue of rats across light-dark cycle every 4 h. IL-6 levels were significantly higher during the light period than during the dark period in the cortex, hippocampus and hypothalamus. In the brainstem, IL-6 levels did not significantly vary across the light-dark cycles. IL-6 levels in the blood and adipose tissues were also significantly higher during the light period than during the dark period. IL-6 levels were positively correlated between the blood and adipose tissue, between hypothalamus and blood, and between the hypothalamus and hippocampus. These observations suggest that IL-6 levels vary across the light-dark cycle among different tissues and that IL-6 levels are elevated both centrally and peripherally during the period predominantly occupied by sleep but decreased during the period that primarily consists of wakefulness.