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Background: Pediatric patients who received hematopoietic stem cell transplantation (HSCT) tend to have high morbidity and mortality. While, the prognostic factors of adult patients received bone marrow transplantation were already known, there is little known in pediatric pateints. This study aimed to identify the prognostic factor for pediatric intensive care unit (PICU) mortality of critically ill pediatric patients with HSCT. Methods: Retrospectively reviewed that the medical records of patients who received HSCT and admitted to PICU between January 2010 and December 2019. Mortality was defined a patient who expired within 28 days. Results: A total of 131 patients were included. There were 63 boys (48.1%) and median age was 11 years (interquartile range, 4–15 years). The most common HSCT type was haploidentical (38.9%) and respiratory failure (44.3%) was the most common reason for PICU admission. Twenty-eight– day mortality was 22.1% (29/131). In comparison between survivors and non-survivors, the number of HSCTs received, sepsis, oncological pediatric risk of mortality-III (OPRISM-III), pediatric risk of mortality-III (PRISM-III), pediatric Sequential Organ Failure Assessment (pSOFA), serum lactate, B-type natriuretic peptide (BNP) and use of mechanical ventilator (MV) and vasoactive inotropics were significant predictors (P<0.05 for all variables). In multivariate logistic regression, the number of HSCTs received, use of MV, OPRISM-III, PRISM-III and pSOFA were independent risk factors of PICU mortality. Moreover, three scoring systems were significant prognostic factors of 28-day mortality. Conclusions: The number of HSCTs received and use of MV were more accurate predictors in pediatric patients received HSCT.