Circadian clocks have emerged to tune the physiology of organisms to periodic changes in the environment in a dynamic fashion. Negative implications of circadian disruptions in humans, animals and plants have encouraged extensive studies of clock-controlled biological processes in various model species. Recently, it has been shown that the transcription-dependent and -independent biological oscillators are largely driven by cellular oxidative cycles that are intrinsically linked with metabolism. Essentially, the clock is viewed as an integrated network that encompasses cytosolic, genetic and metabolic dimensions. Furthermore, in multicellular organisms, the clock network is organized in a tissue-specific manner. Here we discuss questions that remain unanswered: How do these dimensions communicate with each other and how do tissue-specific clocks exchange temporal information within multicellular organisms?