Background and aims: Short bowel syndrome is the major cause of intestinal failure. Patients often require parenteral nutrition for a variable period of time to survive, but there is no consensus on the optimal feeding formula during the weaning from parenteral nutrition. Aim of this study was to retrospectively analyze the development of food allergy in children with short bowel syndrome weaned with a hydrolyzed or an amino acid-based formula. Methods: Clinical data were recorded for each patient. We also collected results of allergy tests of patients who had allergic reactions. Results: Forty-seven children with intestinal failure (26 males; mean age of 4.53±3.85 years), followed-up at the Department of Pediatrics since 2000, were retrospectively evaluated. Thirty-eight of 47 children (80%) had residual bowel<100cm requiring a mean duration of 17.36±6.7 months of parenteral nutrition. In this group 22/38 children were weaned from parenteral nutrition with amino acid-based formula and 16 with hydrolyzed formula. Adverse events were reported in 16/38 children and 10 of these, all weaned with hydrolyzed formula, received diagnosis of cow's milk allergy. None of the 22 children weaned with amino acid-based formula developed allergic reactions. Conclusions: Children weaned with hydrolyzed formula have an increased risk of developing cow's milk allergy in comparison to those weaned with amino acid-based formula and its use may have a role in the prevention of food allergies. The reduced length intestinal residual (<100cm) is a risk factor for the development of allergic reactions.