The molecular basis for biological rhythms is formed by clock genes. Clock genes are functional in the liver, within gastrointestinal epithelial cells and neurons of the enteric nervous system. These observations suggest a possible role for clock genes in various circadian functions of the liver and the gastrointestinal tract through the modulation of organ specific clock-controlled genes. Consequently, disruptions in circadian rhythmicity may lead to adverse health consequences. This review will focus on the current understanding of the role of circadian rhythms in the pathogenesis of gastrointestinal- and hepatic disease such as obesity, non-alcoholic fatty liver disease, alcoholic fatty liver disease and alterations in colonic motility.