Intestinal malrotation is a defect that occurs at the 10th week of gestation. During this stage of development, the intestines normally migrate back into the abdominal cavity following a brief period where they are temporarily located at the base of the umbilical cord. As the intestine returns to the abdomen, it makes two rotations and becomes fixed into its normal position, with the small bowel centrally located in the abdomen and the colon (large intestine) draping around the top and sides of the small intestine. When rotation is incomplete and intestinal fixation does not occur, this creates a defect known as intestinal malrotation.

With intestinal malrotation, the large intestine is located to the left of the abdomen, while the small intestine is on the right of the abdomen. The cecum (beginning of large intestine) and the appendix, which are normally attached to the right lower abdominal wall, are unattached and located in the upper abdomen. In many cases, abnormal tissue referred to as Ladd's bands attaches the cecum to the duodenum (beginning of small intestine) and may create a blockage in the duodenum.

In patients with malrotation, the blood supply to the intestine is channeled through a very narrow supportive structure (mesentery). Since the intestine is not properly fixated, the bowel may twist on its own blood supply; this condition is termed volvulus. When volvulus involves the entire small bowel, it is referred to as mid-gut volvulus. This can result in the loss of most of the intestine. In some case, it may also result in death.

A number of other acute and chronic signs of disease are related to intestinal malrotation and lack of fixation. These include chronic abdominal pain, malabsorption and malnutrition, and subsequent growth disturbances.