Abstract Background/Methods A 32-year retrospective review from 1972 to 2004 analyzed complications and long-term outcomes in children with total colonic aganglionosis (TCA) as they relate to the procedure performed. Results Thirty-six patients (27 boys, 9 girls) had TCA. The level of aganglionosis was distal ileum (26), mid–small bowel (8), midjejunum (1), and entire bowel (1). Enterostomy was performed in 35 of 36. Eight developed short bowel syndrome. Twenty-nine (81%) had a pull-through at 15 ± 6 months (modified Duhamel 20, Martin long Duhamel 4, and Soave 5). Six had a Kimura patch. Postoperative complications (including enterocolitis) were more common after long Duhamel and Soave procedures. Seven (19%; 2 with Down's syndrome) died (3 early, 4 late) from pulmonary emboli (1), sepsis (1), fluid overload (1), viral illness (1), liver failure (1), arrhythmia (1), and total bowel aganglionosis (1). Mean follow-up was 11 ± 9 years (range, 6 months-29 years). Twenty-four (83%) of 29 patients exhibited growth by weight of 25% or more, 21 (91%) of 23 older than toddler age had 4 to 6 bowel movements per day, and 17 (81%) of 21 were continent. In 5 of 6, the Kimura patch provided functional benefit with proximal disease. Conclusion Long-term survival was 81%. The highest morbidity occurred with long Duhamel or Soave procedures. The modified Duhamel is our procedure of choice in TCA. Bowel transplantation is an option for TCA with unadapted short bowel syndrome.