The intestine is exposed constantly to mechanical stimuli, including blood flow or peristalsis. Recently, gut-on-a-chip models have been developed to recapitulate these physiological stresses. In such models, blood flow and peristalsis are simulated by perfusing culture medium through microchannels and applying cyclic suction to vacuum chambers. With these gut-on-a-chips, the effects of mechanical stimuli on the intestinal structure and function have been elucidated. Additionally, gut-on-a-chip models are used to study intestinal diseases, such as infectious diseases, inflammatory bowel disease, and colorectal cancer. Because they accurately recapitulate the pathophysiology of intestinal diseases, research leveraging their use has revealed mechanisms underlying disease onset and progression in the intestine. In this review, we summarize the development of gut-on-a-chip systems and highlight recent research on intestinal diseases using these models.