Objective: To investigate the methylation status of the RUNX family transcription factor 3 ( RUNX3)promoter and its mRNA expression in sepsis patients , and to analyze their relationship with the prognosis of sepsis. Methods: Differentially expressed genes related to sepsis , including RUNX3 , were identified from multiple datasets obtained from the gene expression omnibus (GEO) database. The gene expression and methylation sites were validated. A total of 120 patients with sepsis were included. Clinical data were recorded , and blood samples were collected at enrollment. Relative expression levels of RUNX3 in blood samples and promoter methylation status were detected using qPCR and methylation⁃specific PCR ( MSP) , respectively. Pearson correlation coefficients were used to analyze the correlation between RUNX3 levels in patient blood and clinical indicators. Kaplan⁃Meier analysis was performed to plot survival curves , and Cox proportional hazards regression analysis was conducted to identify factors affecting the prognosis of sepsis patients. Results: Data set analysis revealed that RUNX3 was a differentially methylated gene associated with the prognosis of sepsis. The mRNA expression level of RUNX3 was lower in the non-survivor group compared to the survivor group (P < 0. 05) , and the methylation ratio of RUNX3 was higher in the non-survivor group than in the survivor group (P < 0. 05) . In sepsis patients , RUNX3 mRNA expression levels were negatively correlated with interleukin-6 ( IL-6) , procalcitonin ( PCT) , C-reactive protein ( CRP) , acute physiology and chronic health evaluation ( APACHE Ⅱ ) score , and sequential organ failure assessment ( SOFA) score. Kaplan-Meier analysis showed that the 28-day survival rate in the methylated group was lower than that in the unmethylated group ( P < 0. 05) . Cox regression analysis results indicated that RUNX3 promoter methylation was an independent risk factor for predicting the 28-day prognosis of sepsis patients. Conclusion In sepsis patients , the mRNA levels of RUNX3 were reduced , and the degree of promoter methylation was higher. RUNX3 promoter methylation was an independent risk factor for the 28-day prognosis of sepsis patients and could serve as a prognostic biomarker for sepsis.