Crohn’s disease and ulcerative colitis, together termed inflammatory bowel diseases, are diseases that affect mostly the large and small intestine. They are characterized by inflammation in the intestine that sometimes is more active and, at other times, stays quiet or in remission. The exact reason why people develop these conditions is not known, but several possible reasons have been proposed. As infants develop over the first 2–4 years of life, they establish a pattern of bacteria in their intestine. This varies between different individuals but there are broad patterns. There are also immune cells that develop in the lining of the intestine that is meant to ignore one’s normal bacteria or “good bacteria” but attack potential invading organisms such as those causing food poisoning or “bad bacteria.” For reasons that are not completely clear, in some individuals the immune cells lose the ability to recognize the bacterial pattern as being normal or your own and start making chemicals called cytokines that lead to inflammation and subsequent damage to the lining. We think that there is a definite contribution of genetics to this; a family history of IBD is one of the strongest risk factors for developing disease in an individual. But there are also additional important contributions from the patterns of bacteria in the intestine; for example, studies have shown that the patterns of bacteria in people developing Crohn’s disease or ulcerative colitis are different from those who do not. Additionally there is also an important contribution of the external environment in influencing both the pattern of bacteria and the immune system response. These may include factors such as smoking, diet, use of antibiotics, and stress or depression. There are approximately 1–1.5 million people in the USA with inflammatory bowel disease, so most people know at least one person with IBD.