Segmental aganglionosis Hirschsprung's is an extremely rare condition. Described as a segment of normally ganglionated bowel surrounded proximally and distally by aganglionosis, zonal aganglionosis is of interest because it may cause confusion in interpreting surgical margins. Diagnosis of segmental lesions in Hirschsprung's disease may be missed as it is rarely suspected at initial surgery. We report the case of a 2-week-old baby girl admitted to our clinic for abdominal distension and vomiting. Considering the family history (near total colonic aganglionosis in a 2-month-old sister with unfavorable outcome), the suspicion of Hirschsprung's is raised and serial large intestine biopsies are taken. Intraoperatively, a transverse colon stenosis caused by an incomplete web is noticed and segmental colectomy with anastomosis is performed at this level. Histopathological and immunohistochemical results established the diagnosis of segmental transverse colon aganglionosis, with the presence of ganglia cells in the ascending and descending colon. Subtotal colectomy with ascending colon pull-through was performed with favorable postop evolution. In our patient, the association with a transverse colon stenosis raised suspicion concerning the diagnosis of Hirschsprung's disease, but considering the family history, extended biopsies were taken and the correct diagnosis of zonal aganglionosis was established. Although zonal aganglionosis lesions are extremely rare, this case illustrates the point that the presence of ganglia cells at the resection line is not sufficient to guarantee postoperative function. Extended intestinal biopsies should be included in the algorithm for management of long segment Hirschsprung's disease and will enable the surgeon to correctly detect zonal aganglionosis.