BACKGROUND Drug-eluting stents (DES) are the most common device used in percutaneous treatment of coronary artery disease. Recently, there has been an increased concern regarding their safety profile, in particular the late and very late stent thrombosis rate compared to bare metal stents (BMS). The aim of the study was to compare the reported incidence of late and very late stent thrombosis of DES and BMS in patients from published clinical studies with an extended follow-up period to four years. METHODS A search strategy was developed to identify publications reporting on late or very late thrombosis of BMS and DES available through MEDLINE and Cochrane Library databases. Two independent reviewers appraised eligible studies and extracted data. Odds ratios (OR) were calculated for each outcome and presented with 95% confidence intervals (CI). RESULTS Fourteen randomized controlled trials, which were at least single blinded, were identified. There was no difference in the incidence of late and very late stent thrombosis in patients treated with DES compared with patients treated with BMS (late OR 0.55, 95%CI 0.23 - 1.31 and late/very late OR = 1.08, 95%CI 0.61 - 1.91). CONCLUSIONS The safety profile of DES was similar to BMS in terms of stent thrombosis. We found no evidence of increased risk of late and very late thrombosis for DES.