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Background Compared with the zotarolimus-eluting stent (ZES), the everolimus-eluting stent (EES) has reduced the risk of stent restenosis and thrombosis as found in a number of randomized-controlled trials (RCTs). However, the benefits have been variable. Materials and methods We evaluate the long-term effect of EES and ZES on the risk of stent thrombosis and target lesion revascularization in patients receiving PCI. We identified RCTs by a systematic search of MEDLINE, EMBASE, and Cochrane Database. Results Five RCTs (9853 patients) were included. Overall, EES significantly reduced the risk of target lesion revascularization [odds ratio (OR), 0.77; 95% confidence interval (CI), 0.62-0.95; P=0.01] compared with ZES therapy. However, there was no difference in the risk of target vessel revascularization (OR, 0.93; 95% CI, 0.78-1.10; P=0.38) and definite/probable stent thrombosis (OR, 0.83; 95% CI, 0.56-1.25; P=0.37) between the two groups. Furthermore, the risk of mortality (OR, 1.04; 95% CI, 0.84-1.27; P=0.73), myocardial infarction (OR, 0.95; 95% CI, 0.74-1.23; P=0.70), and major adverse cardiac event (OR, 0.96; 95% CI, 0.84-1.10; P=0.53) was similar between the two groups. Conclusion The new-generation Resolute-ZES and EES have a similar long-term safety and efficacy profile.