OBJECTIVE : Neonates with intestinal atresia (IA) undergo either primary anastomosis (PA) or ostomy creation with secondary anastomosis (SA). Our purpose was to compare outcomes for PA and SA and to assess factors influencing procedure selection. METHODS : We conducted a retrospective cohort study of neonates with IA between 2009 and 2015. Patient characteristics, operative details, and outcomes were collected. Surgeon-level preferences (defined as performing >50% PA or SA) were assessed using logistic regression. RESULTS : Of 92 IA patients, 70 (76.1%) underwent PA and 22 (23.9%) underwent SA. Neonates with PA had shorter hospitalizations (27 days vs. 95 days, p < 0.001), shorter total parenteral nutrition duration (19 days vs. 74.5 days, p < 0.001), and fewer readmissions (33.3% vs. 63.2%, p = 0.024). On multivariable regression analysis, higher Apgar scores (Odds Ratio (OR) 4.16, 95% Confidence Interval (CI) 1.20-14.29) and uncomplicated atresia (OR 3.97, 95% CI 1.37-11.48) were associated with PA. At the surgeon-level, utilization of PA varied from 43.5% to 100%. Surgeon preference is not influenced by the demographic, presentation, or surgical findings of this patient population. CONCLUSIONS : PA has better outcomes than SA. Though procedural selection is influenced by the clinical status of the neonate, however surgeon preference plays a significant role in this clinical decision. METHODS : Level III Treatment Study.