Children who have undergone liver transplantation may develop chronic diarrhea for a number of reasons. Three children who underwent liver transplantation for liver failure, all of whom had had previous biliary and intestinal surgeries and whose postoperative course was marked by signs and symptoms of intestinal malabsorption including chronic diarrhea, are described. Duodenal aspirates showed a panoply of bacterial species, and duodenal histology featured villus atrophy in two: one associated with luminal gram-positive cocci and another with acute and chronic duodenitis. Oral antibiotics cleared the symptoms. Small bowel bacterial overgrowth may need to be considered in children with chronic diarrhea after liver transplantation, especially when previous intestinal surgery has taken place. Long-term antibiotic therapy may be required to effectively eradicate the offending organisms to suppress symptoms.