BackgroundLong‐term outcomes of congenital diarrheas and enteropathies (CODE) are poorly described. We evaluated the morbidity and mortality of children with CODE followed by an intestinal rehabilitation program (IRP) compared to children with short bowel syndrome (SBS).MethodsMatched case‐control study of children with intestinal failure (IF) due to CODE (diagnosed between 2006 and 2020; N = 15) and SBS (N = 42), matched 1:3, based on age at diagnosis and duration of parenteral nutrition (PN). Nutritional status, growth, and IF‐related complications were compared. Survival and enteral autonomy were compared to a nonmatched SBS cohort (N = 177).ResultsFifteen CODE patients (five males, median age 3.2 years) were followed for a median of 2.9 years. Eleven children were alive at the end of the follow‐up, and two achieved enteral autonomy. The CODE group had higher median PN fluid and calorie requirements than their matched SBS controls at the end of the follow‐up (83 vs. 45 mL/kg/day, p = 0.01; 54 vs. 30.5 kcal/kg/day, p < 0.01), but had similar rates of growth parameters, intestinal failure associated liver disease (IFALD), central venous catheter (CVC) complications and nephrocalcinosis. Kaplan–Meier (KM) analyses of 10‐year survival and enteral autonomy were significantly lower in CODE patients compared to the nonmatched SBS population (60% vs. 89% and 30% vs. 87%, respectively; log‐rank p < 0.008).ConclusionsDespite higher PN needs in CODE, rates of IF complications were similar to matched children with SBS. Enteral autonomy and survival rates were lower in CODE patients. Treatment by IRP can mitigate IF‐related complications and improve CODE patient's outcome.