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Extracorporeal Membrane Oxygenation (ECMO) is a life-saving procedure that provides short-term cardiac and respiratory support to people whose heart and lungs are dysfunctional. Growing use of ECMO has expanded the indications beyond acute severe respiratory and cardiac failure to include extracorporeal cardiopulmonary resuscitation and as a bridge for lung transplantation. Usage of ECMO within the pediatric population has seen a number of complications including an acute induction of systemic inflammatory response syndrome (SIRS) and long-term developmental neurological deficits, with an increasing number of children exhibiting neurological morbidities. We hypothesized that ECMO may potentiate the induction of a central nervous system (CNS)-targeting adaptive immune response which may lead to neurological injury. Using a single center prospective observational study, we sampled 20 pediatric ECMO patients and 5 aged-match disease control patients. Peripheral blood mononuclear cells were isolated using the Ficoll-Paque method and relative analysis revealed an increase in helper T-cells that correlated with ECMO treatment alone, while NK-T cells were found to be increased in the presence of CNS injury. Interestingly, we did see a decrease in activated peripheral T-helper cells (CD4+CD161+), and cytotoxic T cells (CD8+CD161+), which were preceded by an increase in activated macrophages (CD14+CD11b+) in ECMO treated patients. Only activated peripheral CD8 T-cells were found to associate with CNS injury. Using the CFSE recall response assay, we tested for CNS specificity by culturing cells with myelin basic protein (MBP), proteolipid lipoprotein (PLP), myelin oligodendrocyte glycoprotein (MOG), NMDA receptor GluN2A, and microtubule associated protein (MAP2) for 7 days and determined a response by measuring CFSE dilution and CD25 expression using flow cytometry. We observed an increased in myelin-targeting B-cells, myelin- and neuronal-targeting CD8 T-cells and no difference in autoreactive CD4 T-cells. In summary, ECMO induces a robust peripheral CNS-targeting adaptive immune response that may predispose a patient to long-term neurological injury.