Basic research programs in the Division of Gastroenterology focus on molecular cell and developmental biology of the intestine, mucosal immunology, and microbial pathogenesis. The GI Cell and Developmental Biology Laboratories are located on two floors of the Enders Research Building and house the labs of four NIH-funded principal investigators, the administrative core and two scientific cores of the Harvard Digestive Diseases Center, and the administrative core of the administrative core of the Harvard Medical School Fellowship in Pediatric GI and Nutrition, directed by Wayne Lencer.

Clinical research in Crohn's disease and ulcerative colitis is conducted at the Center for Inflammatory Bowel Disease.