Light and food are two major environmental factors that impact daily life. Light entrainment is centrally controlled by suprachiasmatic nuclei of the hypothalamus. Food entrainment might require cooperation between the intestine and dorsomedial hypothalamus. Clock genes that are essential for light entrainment also play a part in food entrainment. Understanding the role of clock genes in the entrainment of intestinal functions, as well as in gut–brain communication during food entrainment, will enhance our understanding of gastrointestinal and metabolic disorders. This review highlights recent studies examining light- and food-entrained regulation of plasma lipids and of various intestinal activities and offers insight into the role of the intestine in food entrainment.