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Background: Cardiac surgery-associated acute kidney injury (CS-AKI) and fluid overload (FO) are common among neonates who undergo cardiopulmonary bypass, and increase mortality risk. Current diagnostic criteria may delay diagnosis. Thus, there is a need to identify urine biomarkers that permit earlier and more accurate diagnosis., Methods: This single-centre ancillary prospective cohort study describes age- and disease-specific ranges of 14 urine biomarkers at perioperative time points and explores associations with CS-AKI and FO. Neonates (≤28 days) undergoing cardiac surgery were included. Preterm neonates or those who had pre-operative acute kidney injury were excluded. Urine biomarkers were measured pre-operatively, at 0 to < 8 hours after surgery, and at 8 to 24 hours after surgery. Exploratory outcomes included CS-AKI, defined by the modified Kidney Disease Improving Global Outcomes criteria, and>10% FO, both measured at 48 hours after surgery., Results: Overall, α-glutathione S-transferase, β-2 microglobulin, albumin, cystatin C, neutrophil gelatinase-associated lipocalin, osteopontin, uromodulin, clusterin, and vascular endothelial growth factor concentrations peaked in the early post-operative period; over the sampling period, kidney injury molecule-1 increased and trefoil factor-3 decreased. In the early post-operative period, β-2 microglobulin and α-glutathione S-transferase were higher in neonates who developed CS-AKI; and clusterin, cystatin C, neutrophil gelatinase-associated lipocalin, osteopontin, and α-glutathione S-transferase were higher in neonates who developed FO., Conclusion: In a small, single-centre cohort, age- and disease-specific urine biomarker concentrations are described. These data identify typical trends and will inform future studies.