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Background: Early recognition of septic patients with poor prognosis is important for clinicians to prescribe personalized therapies which include timely fluid resuscitation therapy and appropriate antimicrobial therapy. We aimed to evaluate the effect of the presepsin level on predicting the prognosis of patients with sepsis under the sepsis-3 criteria. Methods: Patients who were diagnosed as sepsis under the sepsis-3 criteria were recruited and assigned to the survivor group and the non-survivor group according to their in-hospital mortality. The two groups’ baseline characteristics were analyzed with Pearson’s chi-square (χ2) test or Kruskal–Wallis test. Binary logistic regression analysis was performed to determine the independent predictors of in-hospital mortality from sepsis. Receiver operating characteristic analysis was conducted to evaluate the efficacy of presepsin in predicting patients’ in-hospital mortality from sepsis. The correlation between presepsin and the Sequential Organ Failure Assessment (SOFA) score was measured with Spearman’s rank correlation coefficient. P-values of less than 0.05 were considered to indicate statistical significance. Results: Overall, 138 patients were included in this study. The presepsin level of the non-survivor group was significantly higher than that of the other group (P=0.000). Binary logistic regression showed that the presepsin level was an independent risk factor of patients’ in-hospital mortality from sepsis (OR =1.221 P=0.026). The presepsin level was positively associated with the SOFA score (ρ=0.396, P=0.000). ROC curve analysis revealed the presepsin level was highly accurate in predicting patients’ in-hospital mortality from sepsis (AUC =0.703, P=0.000). The AUC value of a combination of presepsin and the SOFA score was significantly larger than that of the SOFA score alone (AUC: 0.817 vs 0.793, P=0.041). Conclusions: Presepsin is a prognostic biomarker with high accuracy in predicting the prognosis of sepsis under the sepsis-3 criteria.