Gastrointestinal problems fall into two basic area:

• anatomical anomalies - the structure of the organs is abnormal
• functional disorders - the organs do not work the way they should

The most common anatomical anomalies are:

• aganglionic megacolon - Also called Hirschsprung's disease, this is a condition where parts of the bowel have no nerve cells. Children with this condition can become extremely constipated. Severe cases can be life threatening if left untreated. Hirschsprung's is normally treated by surgically removing the part of the bowel that does not function correctly.

• annular pancreas - This is a condition in which the pancreas is ring-shaped and constricts part of the intestine. Depending on the amount of constriction, this can be a serious medical emergency. This condition is normally treated surgically.

• duodenal atresia and duodenal stenosis - Both of these conditions involve a narrowing of the small intestine the difference being the amount of the narrowing. In duodenal atresia, the first part of the intestine where it connects to the stomach is completely blocked off. Since no food can pass from the stomach into the intestines, this condition must be treated immediately by surgically removing the blocked part of the intestine. A duodenal stenosis involves a narrowing of the intestine. Depending on the amount of narrowing, surgery may be required. In less serious cases, the condition may be managed through diet.

• imperforate anus - This is a condition in which the anus (the external opening of the colon) is blocked. This condition is normally treated with surgery within the first few days after the baby is born.

• tracheo-esophageal fistula - This is a condition where there is an opening between the windpipe and the esophagus. Some children have this condition without developing any problems. Others may require surgery to close the fistula to prevent fluids from travelling from the esophagus into the trachea.
• pyloric stenosis - This is a narrowing of the pylorus, the junction where the stomach empties into the small intestine. This is treated with a simple surgical procedure that usually works very well.

It is important to understand that any of these conditions can occur in any child although they do tend to be more common in children with Down syndrome.
The most common functional disorders are:

• esophageal motility disorders and gastro-esophogeal reflux. Children with Down syndrome often have problems with reflux. Reflux does not mean that the child spits up during or after a feeding. In most cases, this simply means the child has swallowed air. Reflux can occur because the esophagus is having trouble propelling food into the stomach or it may occur because the stomach is emptying too slowly. Persistent reflux may cause serious problems since the stomach contents are highly acidic and can damage the esophagus, larynx, or trachea. If the child aspirates stomach acids, they may gag or cough just after feeding. Reflux is normally treated with medicines to reduce stomach acidity and to help move food through the stomach faster. In many cases, the child may grow out of the problem.

• malabsorption disorders - Children with Down syndrome sometimes have a condition called celiac disease in which the intestines lose the ability to absorb nutrients. This condition is normally treated by eliminating gluten from the diet. There are other malabsorption disorders but children with Down syndrome are no more likely to have these conditions then the rest of the population. Some children with Down syndrome may have trouble absorbing certain vitamins. If the child is not growing well or has an increased number of ordinary infections that are difficult to cure, they may have a vitamin absorption problem. A blood test can help to determine if this is a problem.