Circadian rhythms are the daily patterns that occur within an organism, from gene expression to behavior. These rhythms are governed not only externally by environmental cues but also internally, with cell-autonomous molecular clock mechanisms present nearly ubiquitously throughout the cells of organisms. In more complex organisms, it has been suggested that the clock mechanisms serve varied functions depending on the tissue in which they are found. By disrupting core circadian gene function in specific tissues of animal models, the various roles of the circadian clock in differing tissues can begin to be defined. This review provides an overview of the model organisms used to elucidate tissue-specific functions of the molecular circadian clock. © 2014 IUBMB Life, 66(1):34–41, 2014.