Old-generation drug-eluting coronary stents (o-DES) have despite being safe and effective been associated with an increased propensity of late stent thrombosis (ST). We evaluated ST rates in o-DES, new-generation DES (n-DES) and bare metal stents (BMS) the first year (< 1 year) and beyond 1 year (> 1 year). We evaluated all implantations with BMS, o-DES (Cordis Cypher, Boston Scientific Taxus Libert, and Medtronic Endeavor) and n-DES in the Swedish coronary angiography and angioplasty registry (SCAAR) between 1 January 2007 and 8 January 2014 (n = 207 291). All cases of ST (n = 2 268) until 31 December 2014 were analyzed. The overall risk of ST was lower in both n-DES and o-DES compared with BMS up to 1 year (n-DES versus BMS: adjusted risk ratio (RR) 0.48 (0.41-0.58) and o-DES versus BMS: 0.56 (0.46-0.67), both p < 0.001). From 1 year after stent implantation and onward, the risk for ST was higher in o-DES compared with BMS [adjusted RR, 1.82 (1.47-2.25], p < 0.001). N-DES were associated with similar low ST rates as BMS from 1 year and onward [adjusted RR 1.21 (0.94-1.56), p = 0.135]. New-generation DES were associated with lower ST rates in comparison to BMS during the first-year post-stenting. After 1 year, n-DES and BMS were associated with similar ST rates. This study was a retrospective observational study and as such did not require clinical trial database registration.