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Background Hemodialysis (HD) is the most important renal replacement therapy for patients with end-stage kidney disease (ESKD). Systemic inflammation is a risk factor of mortality in HD patients. Neutrophil-to-lymphocyte ratio (NLR), monocyte-to-lymphocyte ratio (MLR), and platelet-to-lymphocyte ratio (PLR) are new inflammatory markers. However, previous studies have inconsistent conclusions about the predictive value of NLR, MLR and PLR on mortality of HD patients. The aim of this study was to establish an inflammation scoring system by including NLR, MLR and PLR, and evaluate the association between the inflammation score and all-cause and cardiovascular mortality in HD patients. Methods In this single center retrospective cohort study, 213 incident HD patients from January 1, 2015 to December 31, 2020 were included. Baseline demographic and clinical data and laboratory measurements were collected. According to the optimal cut-off values, NLR, MLR and PLR were assigned 0 or 1 point, respectively. Then, the inflammation score was obtained by adding the NLR, MLR and PLR scores. All patients were followed until July 31, 2021. The associations of the inflammation score with all-cause and cardiovascular mortality were assessed by multivariable-adjusted Cox models. Results Of 213 patients, the mean (± SD) age was 56.8 ± 14.4 years, 66.2% were men, and 32.9% with diabetes. The primary cause of ESKD was mainly chronic glomerulonephritis (46.5%) and diabetic nephropathy (28.6%). The median inflammation score was 2 (interquartile range = 1–3). During a median 30 months (interquartile range = 17–50 months) follow-up period, 53 patients had died, of which 33 deaths were caused by cardiovascular disease. After adjusting for demographics, primary diseases and other confounders in multivariable model, the inflammation score = 3 was associated with a hazard ratio for all-cause mortality of 4.562 (95% confidence interval, 1.342–15.504, P = 0.015) and a hazard ratio for cardiovascular mortality of 4.027 (95% confidence interval, 0.882–18.384, P = 0.072). Conclusion In conclusion, an inflammation scoring system was established by including NLR, MLR and PLR, and the higher inflammation score was independently associated with all-cause mortality in HD patients.