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In our experience, the Santulli procedure (SP) can improve bowel recovery in congenital intestinal malformations, necrotizing enterocolitis (NEC), and bowel perforation. All cases managed at our institution using SP between 2012 and 2017 were included in this study. Forty-one patients underwent SP (median age: 39 (0–335) days, median weight: 2987 (1400–8100) g) for intestinal atresia (51%, two gastroschisis), NEC (29%), midgut volvulus (10%), Hirschsprung’s disease (5%), or bowel perforation (5%), with at least one intestinal suture below the Santulli in 10% of cases. The SP was performed as a primary procedure (57%) or as a double-ileostomy reversal. Anal-stool passing occurred within a median of 9 (2–36) days for 95% of patients, regardless of the diversion level or the underlying disease. All three patients requiring repeated surgery for Santulli dysfunction had presented with stoma prolapse (p < 0.01). Stoma closure was performed after a median of 45 (14–270) days allowing efficient transit after a median of 2 (1–6) days. After a median follow-up of 2.9 (0.7–7.2) years, two patients died (cardiopathy and brain hemorrhage), full oral intake had been achieved in 90% of patients, and all survivors had normal bowel movement. Whether used as primary or secondary surgery, the SP allows rapid recovery of intestinal motility and function.