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Background: Acute kidney injury (AKI) is common in critically ill children with significant mortality and morbidity. Serum creatinine is an insensitive and late biomarker compared to newly proposed AKI biomarkers., Methods: Prospective study in pediatric intensive care unit (PICU) over three months to compare between serum cystatin-C (s-Cys-C) and urinary neutrophil gelatinase-associated lipocalin (uNGAL) as AKI biomarkers at multiple time points with pediatric risk, injury, failure, loss, end-stage renal disease (pRIFLE) classification in diagnosing AKI., Results: Forty children were recruited. Of these 40 children, 22 developed AKI according to pRIFLE criteria. There was no significant difference between AKI and non-AKI in age (P = 0.29). Post cardiac surgery, renal insult was the main cause of AKI (27.3%). There was a twofold increased risk of incident AKI in those patients with high baseline uNGAL at PICU admission and almost a fourfold increased risk in patients with high baseline s-Cys-C at PICU admission. uNGAL levels were highly predictive of AKI during the follow-up period [area under the curve (AUC) = 0.76, 95% confidence interval (CI) 0.61-0.92]. The cutoff point with the highest correctly classified proportion was 223 ng/mL (≥ 12 centiles) which correctly predict 80.0% patients with AKI, with a corresponding sensitivity of 72.7% and a specificity of 89.9%. AUC for s-Cys-C was 0.86 (95% CI 0.75-0.97), and the highest correctly classified proportion was 1009 µg/L (≥ 13 centiles); 75% of patients with AKI, with a corresponding sensitivity of 63.6% and a specificity of 88.9%., Conclusion: uNGAL and s-Cys-C predicts AKI early in critically ill children.