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Several meta-analyses have shown no significant difference in stent thrombosis (ST) between sirolimus eluting stents (SES) and paclitaxel eluting stents (PES). However, other meta-analyses have found SES to be superior to PES. Therefore, to solve this issue, we aim to compare the clinical outcomes between SES and PES during a follow-up period of about 1 or more years.We have searched Medline and EMBASE for randomized controlled trials (RCTs) comparing SES with PES. These RCTs have been carefully analyzed and then different types of ST including ST defined by the Academic Research Consortium (ARC), acute ST, late and very late ST have all been considered as the clinical endpoints in this study. A follow-up period of about 1 year, between 1 and 2 years as well as a longer follow-up period between 1 and 5 years have been considered. Data were retrieved and combined by means of a fixed-effect model because of a lower heterogeneity observed among the results. Odd ratios (OR) and 95% confidence intervals (CIs) were calculated and the pooled analyses were performed with RevMan 5.3 software.Twenty-nine studies from 19 RCTs comprising of 16,724 patients (8115 patients in the SES group and 8609 patients in the PES group) satisfied the inclusion criteria and were included in this meta-analysis. No significant differences in ST have been observed between SES and PES. Results were as follow: definite ST with OR: 0.87; 95% CI: 0.64–1.18, P = 0.36; probable ST with OR:0.72; 95% CI: 0.42–1.21, P = 0.21; definite, probable and/or possible ST with OR: 0.94; 95% CI: 0.75–1.17, P = 0.57; acute ST with OR: 0.99; 95% CI: 0.38–2.56, P = 0.98; subacute ST with OR: 0.72; 95% CI: 0.41–1.25, P = 0.25; early ST with OR: 0.81; 95% CI: 0.53–1.25, P = 0.34; late ST with OR: 0.72; 95% CI: 0.39–1.34, P = 0.30; very late ST with OR: 1.02; 95% CI: 0.72–1.44, P = 0.92; and any ST with OR: 0.86; 95% CI: 0.69–1.07, P = 0.18. Long-term ST between 1 and 5 years with OR: 0.93; 95% CI: 0.71–1.22, P = 0.60 was also not significantly different.No significant difference in ST has been observed between patients treated with either SES or PES. Hence SES and PES can both be considered almost equally effective.