We report the case of a 6-month-old boy who developed chronic intestinal pseudo-obstruction soon after birth. A rectal biopsy demonstrated immaturity of the neuronal cells in the enteral ganglion. His clinical course was stressful, with remission and exacerbation despite conservative treatment with daily bowel irrigation, prokinetic agents, and parenteral nutrition. Since the infant developed serious enterocolitis associated with the increased severity of his bowel obstruction, and no substantial gain in body weight was observed, a loopileostomy was performed based on X-ray findings with radio-opaque markers, which were employed to evaluate the whole gut transit time. The radio-opaque markers proved extremely useful for determining which loop of the ileum should be utilized for the ileostomy.