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Blood pressure variability (BPV), defined as the degree of variation between discrete blood pressure readings, is associated with poor outcomes in acute care settings. Acute kidney injury (AKI) is a common and serious postoperative complication of cardiac surgery with cardiopulmonary bypass (CPB) in children. No studies have yet assessed the association between intraoperative BPV during cardiac surgery with CPB and the development of AKI in children. A retrospective chart review of children undergoing cardiac surgery with CPB was performed. Intraoperative BPV was calculated using average real variability (ARV) and standard deviation (SD). Multiple regression models were used to examine the association between BPV and outcomes of AKI, hospital and intensive care unit (PICU) length of stay, and length of mechanical ventilation. Among 231 patients (58% males, median age 8.6 months) reviewed, 51.5% developed AKI (47.9% Stage I, 41.2% Stage II, 10.9% Stage III). In adjusted models, systolic and diastolic ARV were associated with development of any stage AKI (OR 1.40, 95% CI 1.08–1.8 and OR 1.4, 95% CI 1.05–1.8, respectively). Greater diastolic SD was associated with longer PICU length of stay (β 0.94, 95% CI 0.62–1.2). When stratified by age, greater systolic ARV and SD were associated with AKI in infants ≤ 12 months, but there was no relationship in children > 12 months. Greater BPV during cardiac surgery with CPB was associated with development of postoperative AKI in infants, suggesting that BPV is a potentially modifiable risk factor for AKI in this high-risk population.