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To determine the potential value and suitability of Bishop-Koop procedure (BK) compared to divided stoma (DS) in neonates with meconium ileus (MI), congenital intestinal atresia (CIA), and necrotizing enterocolitis (NEC).A retrospective data collection from 2000 to 2019 on neonates undergoing BK and DS formation and closure for MI, CIA, and NEC was conducted. Ostomy related complications following both procedures were analyzed.One hundred two consecutive patients managed with a BK (n = 57, 55.8%) and DS (n = 45, 44.2%) for MI (n = 38, 37.2%), CIA (n = 31, 30.5%), and NEC (n = 33, 32.3%) were analyzed. Mean operating time for ostomy creation did not differ significantly between BK and DS groups (156 ± 54 vs 135 ± 66.8 min, P = .08). The prevalence of stoma-related complications following BK and DS formation was 8.7% and 31.1%, respectively (P = .005). The complication rate after BK and DS closure was 3.5% and 6.7%, respectively (P = .65). The operating time for ostomy reversal and length of hospital stay after stoma closure were significantly shorter in BK group (82.2 ± 51.4 vs 183 ± 84.5 min and 5.5 ± 2.7 vs 11.3 ± 3.9 days, P < .001).BK procedure is safe, reliable, and suitable technique in neonatal surgery with low complications rate following ostomy creation as well as shorter operating time and length of hospital stay after ostomy closure compared to DS ostomies. Surgeons should keep this technique as an alternative approach in their repertoire.