Circadian rhythms ensure that physiological processes occur at the most biologically meaningful time. The circadian timing in the gastrointestinal tract involves interlocking transcriptional and translational feedback loops that culminate in the rhythmic expression and activity of a set of clock genes and related hormones. The suprachiasmatic nucleus and peripheral core molecular clocks oscillate every 24 hours and are responsible for the periodic activity of various segments and transit along the gastrointestinal tract. Environmental cues may alter or reset these rhythms to align them with new circumstances. Colonic motility also follows a circadian rhythm with reduced nocturnal activity. Healthy humans have normal bowel motility during the day, frequently following awakening or following a meal, with minimal activity during the night. Maladjusted circadian rhythms in the bowel have been linked to digestive pathologies, including constipation and irritable bowel syndrome. Our advanced knowledge of the link between the circadian clock and gastrointestinal physiology provides potential therapeutic approaches for the treatment of gastrointestinal diseases. This review seeks to establish evidence for the correlation between circadian rhythm, bowel movements and digestive health, and examine the implications of disrupted circadian rhythms on gut physiology.