Introduction: Congenital microvillus inclusion disease (CMID) causes serious watery diarrhea with nonspecific loss of ionic electrolytes, and the small bowel transplantation (SBTx) is indicated for this disease as an organic therapy. Here we report the long term follow-up of the growth of a case of CMID who had received the growth hormone (GH) therapy and underwent living-related SBTx. Methods: The patient is a 19-year-old boy. On the first day of birth he presented life-threatening dehydration and acidosis caused by severe watery diarrhea. At the age of two months, total parenteral nutrition (TPN) was introduced. Daily stool volume exceeded 2500 ml and extra-supply of NaCl, K+, and HCO3- was necessary. Almost totally depending on TPN, his growth had kept within normal range (height S.D. score: −2.0), but his growth rate after the age of 10 years declined. At the age of 11, he had a pathological bone fracture caused by phosphopenic rickets, and extra phosphorus was added to the TPN. Protein loss from intestine and hypoproteinemia were not seen. Results: At the age of 13, based on the diagnosis as GH deficiency, GH therapy was started, and initial pubertal signs appeared since 14 years old, but his growth rate was not improved (11 cm/2.7 yrs). At the age of 16 he received transplantation of an ileal graft (150 cm in length) from his grandmother. His histologically affected ileo-cecal valve and colon were reserved. At the time of transplantation his height S.D. score was -4.5. Postoperative immunosuppressive therapy consisted of a combination of tacrolimus, daclizumab, cyclophosphamide, and low-dose steroid. Thirteen months after the SBTx, free from TPN, he fed himself totally perorally, and GH therapy was restarted. After that his growth rate dramatically improved (19 cm/2.1 yrs, final height S.D. score: −2.2). Conclusion: The dramatic response of the growth to GH therapy after SBTx and establishment of peroral nutrition found in the case of CMID leads the following hypotheses: i) in CMID some growth-related factors may be lost from the affected small intestinal mucosa, ii) establishment of peroral feeding and the digestive and absorptive process from normal small intestinal mucosa may generate some growth-related factors which cannot be supplied by current TPN prescription.