Aims & Objectives: Extracorporeal membrane oxygenation after surgery for congenital heart disease provides hemodynamic support to patients when their myocardial function is affected. This therapy has been associated with a higher risk of complications like bleeding or infections. It is not known if the type of microorganisms isolated in infected patients is associated with worse outcomes. The objective of this study was to analyze the mortality related to the microorganism isolated in children who require ECMO in the immediate postoperative period following surgery for congenital heart disease. Methods: This was a retrospective cohort study from January 2014 to December 2021 in hospital in Colombia. Results: 3,307 surgeries for congenital heart disease were performed during this period. Of these, 108 (3.3%) required ECMO. Bacteria were isolated in 89.4%.The incidence of infection was 14.5 cases per 1,000 days of ECMO. The mortality of infected patients was 54.1%. Isolation of Gram-negative in cultures was associated with higher odds of dying compared with other isolations, regardless of age and type of heart disease (aOR 6.92 95% CI 1.91 -25.02; p<0.01). The most commonly isolated Gram-negative organism was Klebsiella pneumoniae, which was associated with longer mechanical ventilation [26 days (IQR 18.2-31.0) vs. 11 days (IQR 8.0-15.0); p<0.01]. Conclusions: In this study, we found that infections occurred in 1 out of 3 children on ECMO following corrective surgery for congenital heart disease. The presence of a Gram-negative microbe as the cause of infection in any sample was associated with increased odds of mortality, regardless of age or the type of heart disease. Keywords: Extracorporeal Organ Support. ECMO, pediatric intensive care, congenital heart disease, nosocomial infections