Aims: Data are limited on the prognostic impact of stent thrombosis and in-stent restenosis in patients treated with coronary stents. We examined the prognostic impact of stent thrombosis and in-stent restenosis in patients treated with percutaneous coronary intervention (PCI). Methods and results: All patients who underwent stent implantation from 2002 to 2005 were identified in the Western Denmark Heart Registry. The hazard ratio (HR) for death associated with stent thrombosis or in-stent restenosis was estimated with a Cox regression analysis with stent thrombosis or in-stent restenosis as time-dependent variables. A total of 12,277 patients were treated with stent implantation. Stent thrombosis was observed in 111 (0.9%) patients and in-stent restenosis in 503 (4.1%) patients within 12 months after the index PCI. Occurrence of stent thrombosis was associated with an increased risk of death (HR=2.71 [95% CI: 1.72-4.27]) compared to cases without stent thrombosis. In-stent restenosis had no substantial impact (HR=1.17 [95% CI: 0.79-1.75]). However, in-stent restenosis presenting as non-ST-segment elevation myocardial infarction (NSTEMI) was associated with a greater mortality risk compared with presentation of in-stent restenosis without myocardial infarction (HR=3.11 [95% CI: 1.08-8.69]; p=0.036). Conclusions: The occurrence of stent thrombosis and in-stent restenosis presenting with NSTEMI increased the mortality risk threefold whereas in-stent restenosis without myocardial infarction was not associated with an increased mortality risk.