The most common complication that arises from Crohn's is, due to excessive inflammation, swelling, and scar tissue, blockages or obstructions that occur throughout the digestive tract. As the walls of the bowel thicken, the intestinal passages become significantly narrower and more easily blocked. Symptoms of obstruction usually include abdominal cramping, bloating, and distending. Vomiting is also common. Inflammation may be controlled by medication, but if swelling is not reduced adequately enough for the blockage to pass, surgery may be required. Also, surgery to remove the affected area of intestine may be necessary if the blockage occurs frequently.

Another complication common among Crohn's sufferers is the formation of ulcers or sores within the intestinal tract. Sometimes deep ulcers may progress into fistulas, which may channel into the surrounding tissue of the vagina, bladder, or skin, or may join different areas of the intestine. Fistulas may lead to further complications if they become infected, such as excessive abdominal pain and fever. If they are relatively small, they may be treated by medication, but larger or more severe fistulas may require surgery. Another issue that arises occasionally is the formation of abscesses, or pockets of pus, from fistulas. These areas of infection typically require drainage through a catheter or surgical drain. Areas of around the rectum are often affected by abscesses. Another complication is the development of fissures, or cracks, around the lining of the anus. As a result of excessive blood loss from ulcers and sores, anemia is also common.

From inadequate dietary intake, excessive loss of nutrients through vomiting and diarrhea, and poor absorption of food, nutritional deficiencies and malnutrition are often a complication arising from Crohn's Disease. Although not typically encountered unless the disorder occurs in extensive durations, these deficiencies may include lack of vitamins, proteins and calories. Luckily, nutritional supplementation is usually effective in the treatment of malnutrition. This may include injections of the missing nutrients or ingesting it in liquid or pill form. Because supplements are usually in concentrated forms, they are more effective and absorbed in higher quantities than available in food intake alone.

An often forgotten complication of Crohn's Disease is the psychological impact it has on its sufferers. Depression, anxiety, and tension are common among patients.