From photosynthetic bacteria to mammals, the circadian clock evolved to track diurnal rhythms and enable organisms to anticipate daily recurring changes such as temperature and light. It orchestrates a broad spectrum of physiology such as the sleep/wake and eating/fasting cycles. While we have made tremendous advances in our understanding of the molecular details of the circadian clock mechanism and how it is synchronized with the environment, we still have rudimentary knowledge of its connections to diurnal physiology. One reason for this lack of understanding is the sheer size of the output network. Transcriptomic studies have identified more than 2000 clock-controlled genes (CCGs) with rhythmic expression patterns. Toward exploring this network in vertebrates, we selected Danio rerio as model system. As an initial step, by combining liver tissue sampling in a 2-days time series, transcription profiling using oligonucleotide arrays and bioinformatics analysis, we profiled rhythmic genes and identified several thousands rhythmic genes including ~200 clock-controlled transcription factors (CCTFs). Comparative transcriptomics between Zebrafish, mice and human datasets revealed interesting features of the output network. The results from a global analysis of the union and intersection between the datasets suggest that a large portion of the CCTFs may be involved in circadian gating. Undoubtedly, the Zebrafish model system will help identify new vertebrate outputs and their regulators and provide leads for further characterization of the cis-regulatory network.