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Failure to recognize intestinal malrotation in adults can cause complications during surgeries, especially those with a limited operative field. We report a case of short bowel syndrome caused by mistaken creation of a loop enterostomy in the jejunum due to undiagnosed intestinal malrotation.A 72-year-old man underwent a laparoscopic right hemicolectomy and ileocolostomy because of complicated diverticulitis. Six days after the surgery, he received laparoscopic exploration because of anastomotic leak, and a laparoscopic loop ileostomy was also performed as a protective diversion stoma. One month after surgery, he complained of severe diarrhea from the enterostomy after food and water intake. An upper gastrointestinal and small bowel series revealed that the duodenojejunal junction (DJJ) did not cross the midline and there was a short distance between the DJJ and the enterostomy in the right lower quadrant.Short bowel syndrome caused by mistaken creation of a loop enterostomy in the jejunum due to undiagnosed intestinal malrotation.Total parental nutrition was used and the loop enterostomy was closed 3 months after the initial surgery.The patient was discharged uneventfully 2 weeks after the loop enterostomy.Intestinal malrotation in adults is often encountered during routine radiological examinations. However, it may cause complications during surgery if ignored. Radiologists should keep in mind that complications may occur if a complete presurgical evaluation of intestinal malrotation is not performed, and surgeons should take caution when performing surgeries, especially those with a limited operative field.