Short bowel syndrome (SBS) is the leading cause of intestinal failure in children, a condition of absence of sufficient bowel to meet the nutritional and metabolic needs of a growing individual. The treatment of patients in this situation is based on the association of parenteral and enteral nutrition for prolonged periods of time until intestinal rehabilitation occurs with complete enteral nutrition autonomy. Six consecutive cases of children with SBS (residual intestinal length of 5 cm to 75 cm) were managed with this program and were diagnosed with associated hypothyroidism during the treatment (ages at the diagnosis 5 months to 12 years). All patients were successfully treated with oral hormone reposition therapy and in one patient, the replacement was performed via rectal enemas due to a complete absence of small bowel. Although iodine deficiency associated to long-term parenteral nutrition is a well-known condition, this is the first report in the literature about an expressive number of patients with hypothyroidism detected in patients with SBS during the prolonged treatment for intestinal rehabilitation.