Two consecutive short gut babies with a residual small intestinal length of 44 and 46 cm, respectively, were managed initially by total parenteral nutrition and oral feedings begun around the fifth week postoperatively. Uncontrollable diarrhea, malabsorption, and failure to thrive made the early management of these babies a difficult problem. The two infants developed clinical features of hypothyroidism at the age of 4 and 6 mo, respectively. Hypothyroxinemia was confirmed by repeated detection of low serum levels of T4. Hormonal treatment resulted in clinical recovery and normalized T4 values. Thyroid function has remained normal after discontinuation of treatment, underlining the transient nature of hypothyroidism. Early recognition and therapy of this previously unreported association is essential in order to prevent mental retardation.