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Background MicroRNA (miRNA) expression profiles in endothelial progenitor cells (EPCs) contribute to EPC dysfunction in patients suffering from coronary artery disease. However, it remains unclear whether miRNA expression in EPCs is associated with the prognosis of chronic heart failure (CHF) secondary to ischemic cardiomyopathy (ICM) or non-ischemic cardiomyopathy (NICM). Methods and results One hundred six patients with CHF (55 ICM and 51 NICM) and 30 healthy controls were followed until the end of 24months or when the end point was obtained (cardiovascular death). The miRNA expression profile was analyzed by TaqMan Human MicroRNA Array Set v2.0 in 30 randomly assigned samples (ICM=10, NICM=10, and healthy controls=10). During the 24-month follow-up, 26 patients died from cardiovascular disease. Sixteen miRNAs (miR-126, miR-508-5p, miR-34a, miR-210, miR-490-3p, miR-513-5p, miR-517c, miR-518e, miR-589, miR-220c, miR-200a*, miR-186*, miR-7i*, miR-200b*, miR-595, and miR-662) were found to be differentially expressed between ICM and NICM patients. Survival analysis showed that miR-126 and miR-508-5p levels in EPCs were independent prognostic factors ( P =0.003; HR (hazard ratio): 0.19; 95% CI (confidence intervals): 0.06–0.58, P =0.002; HR: 2.292; 95% CI: 1.37–3.84) for the outcome of ICM or NICM patients with CHF. Pathway enrichment analysis showed that the angiogenesis pathway was the most likely pathway regulated by miR-126 and miR-508-5p. Conclusions The miRNAs miR-126 and miR-508-5p are associated with the outcome of ICM and NICM patients with CHF. These two miRNAs could be useful in the diagnosis of CHF patients, and might provide novel targets for prevention and treatment of CHF.