Background: Cystatin C (Cys C) has been implicated as a prognostic marker in cardiovascular disease. The aim of this study was to evaluate the value of Cys C as a marker of acute kidney injury (AKI) in acute heart failure (AHF), the impact of Cys C and N-terminal probrain natriuretic peptides (NT-proBNP) on in-hospital and 12 months mortality were also investigated.Materials and Methods: A total of 162 patients with AHF were enrolled. NT-proBNP, Cys C, serum creatinine (Scr), blood urea nitrogen (BUN) and parameters of echocardiography were measured for analyze. The in-hospital and 12 months mortality was analyzed.Results: There was 28 (17%) of all AHF patients with AKI. Compared with no-AKI patients, the levels of Cys C (1.51±0.34vs. 1.32±0.29, P=0.003) and NT-proBNP (8163.87±898.06 vs. 5922.45±576.73, P=0.001) were higher in AKI patients. Higher levels of NT-proBNP (odds ratio (OR)=1.92, 95% confidence interval (CI): 2.19-10.98, P=0.018, OR=4.31, 95% CI: 2.35-9.82,P=0.002, respectively) and Cys C (OR=1.48, 95% CI: 1.75-4.16, P=0.027, OR=2.72, 95% CI: 1.92-4.28, P=0.017, respectively)were independent association with the in-hospital and 12 months mortality. Cys C was positively correlated with NT-proBNP (r=0.87, P<0.001). Combining tertiles of Cys C and NT-proBNP improved risk stratification further. Compared with patients without AKI CysC, patients with AKI cysC was associated with higher in-hospital (7.28 vs. 10.134, P=0.002) and 12-month mortality (13.28 vs. 32.134, P=0.001).Conclusion: Cys C was not only a promising risk marker in patients hospitalized for AHF, but also an independent predictor of 12-month mortality. Combining tertiles of Cys C and NT-proBNP could be used to distinguish the mortality risk identification of patients with AHF. AKI was an independent predictor of in-hospital and 12-month mortality.