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Abstract Purpose The study was aimed to assess the prognostic power The Pediatric Risk of Mortality-3 (PRISM-3) and the Pediatric Index of Mortality-3 (PIM-3) to predict in-hospital mortality in a sample of patients admitted to the PICUs. Design and methods The study was performed to include all children younger than 18 years of age admitted to receive critical care in two hospitals, Mashhad, northeast of Iran from December 2017 to November 2018. The predictive performance was quantified in terms of the overall performance by measuring the Brier Score (BS) and standardized mortality ratio (SMR), discrimination by assessing the AUC, and calibration by applying the Hosmer-Lemeshow test. Results A total of 2446 patients with the median age of 4.2 months (56% male) were included in the study. The PICU and in-hospital mortality were 12.4 and 16.14%, respectively. The BS of the PRISM-3 and PIM-3 was 0.088 and 0.093 for PICU mortality and 0.108 and 0.113 for in-hospital mortality. For the entire sample, the SMR of the PRISM-3 and PIM-3 were 1.34 and 1.37 for PICU mortality and 1.73 and 1.78 for in-hospital mortality, respectively. The PRISM-3 demonstrated significantly higher discrimination power in comparison with the PIM-3 (AUC = 0.829 vs 0.745) for in-hospital mortality. (AUC = 0.779 vs 0.739) for in-hospital mortality. The HL test revealed poor calibration for both models in both outcomes. Conclusions The performance measures of PRISM-3 were better than PIM-3 in both PICU and in-hospital mortality. However, further recalibration and modification studies are required to improve the predictive power to a clinically acceptable level before daily clinical use. Practice implications The calibration of the PRISM-3 model is more satisfactory than PIM-3, however both models have fair discrimination power.