PURPOSE: Establishment of evidence-based best practices for preventing surgical site infection (SSI) in neonates is needed. SSI in neonates, especially those with a low birth weight, is potentially life-threatening. We aimed to identify risk factors associated with SSI in neonates. METHODS: A retrospective review was performed using 2007-2016 admission data from our institution. Neonatal patients who were admitted to the neonatal intensive care unit and underwent surgery were evaluated for a relationship between development of SSI and perinatal or perioperative factors and methicillin-resistant Staphylococcus aureus (MRSA) colonization during hospitalization. RESULTS: One hundred and eighty-one patients were enrolled in this study. Overall SSI incidence was 8.8%. Univariate analysis showed that SSI was significantly more frequent in both patients with contaminated or dirty wound operations and patients with MRSA colonization during hospitalization. Both of these factors were identified as independent risk factors for SSI by multivariate analysis [hazard ratio (HR): 6.1, 95% confidence interval (CI) 2.0-19.9; HR: 3.3, 95% CI 1.1-10.4, respectively]. CONCLUSIONS: This study identified contaminated or dirty wound operations and MRSA colonization during hospitalization as risk factors for SSI in neonates. MRSA colonization may be a preventable factor, unlike previously reported risk factors.