Objective: To identify factors associated with development of symptomatic infection in infants colonized with methicillin-resistant Staphylococcus aureus (MRSA) in the Neonatal Intensive Care Unit (NICU). Study design: This case-control study was performed at St. Louis Children’s Hospital NICU from 2009 to 2019. The MRSA-colonized infants who developed symptomatic MRSA infection (cases) were matched 1:3 with MRSA-colonized infants who did not develop infection (controls). Demographics and characteristics of NICU course were compared between groups. Longitudinal information from subsequent hospitalizations was also obtained. Results: Forty-two infected cases were compared with 126 colonized-only controls. Cases became colonized earlier in their NICU stay, were less likely to have received mupirocin for decolonization, and had a longer course of mechanical ventilation than controls. Longitudinally, cases had a more protracted NICU course and were more likely to require hospital readmission. Conclusion: Progression from MRSA colonization to symptomatic infection is associated with increased morbidity and may be mitigated through decolonization.