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Cardiac resynchronization therapy (CRT) has been established as a treatment for patients with chronic heart failure (HF). We tested the hypothesis that assessment of peripheral endothelial function is associated with the long-term outcome of CRT and its linkage to coronary flow reserve (CFR) was also investigated.From 2010, a total of 34 consecutive patients implanted with CRT for the treatment of advanced HF were evaluated at baseline (immediately before CRT) and 6–8 months after CRT. Endothelial function was evaluated by measurement of reactive hyperemia peripheral arterial tonometry (RH-PAT). In 24 of 34 patients, CFR was determined by transthoracic echocardiography.Based on the receiver-operating characteristic curves, depressed RH-PAT index (RHI) was defined as ≤1.5. Accurate follow-up information during the mean of 343 ± 120 days was obtained in 20 preserved RHI group (mean age 66 ± 1.8 years) and 14 depressed RHI group (71 ± 2.2 years). Kaplan-Meier survival analysis demonstrated that depressed RHI group had higher prevalence of new hospitalization due to HF progression (log-rank 5.40). Cox proportional hazards regression analysis revealed that the baseline log brain natriuretic peptide (hazard ratio 5.95) and the baseline RHI value (hazard ratio 0.066) were independently associated with the incidence of new hospitalization due to HF progression. The baseline RHI values were positively correlated with the 6–8 months change of CFR (R = 0.434, P = 0.0343).Our results suggest that the baseline peripheral endothelial function could predict the long-term outcome of CRT. The results also suggest that improvement of coronary microcirculation might be associated with the better baseline endothelial function.