Clinical trial data have supported the safety and efficacy of drug-eluting stents (DES) in the treatment of patients with ST-segment elevation myocardial infarctions (STEMIs), but contemporary “real-world” registry data regarding the late safety profiles of DES are limited. This prospective registry-based study included 1,569 consecutive unselected patients with STEMIs who underwent emergency primary percutaneous coronary intervention from January 2001 to December 2009. Of the study cohort, 200 patients (12.7%) received DES, while 1,369 patients (87.3%) underwent bare-metal stent (BMS) placement. The primary end points of the study were all-cause mortality and target vessel revascularization at 1, 2, and 3 years. Survival status was assessed by municipal civil registries. Repeat revascularization procedures were prospectively collected in the hospital database. All-cause mortality was significantly lower in the DES group at 3 years (4.2% vs 13.5%, p = 0.007) compared to BMS-treated patients, but DES use was not an independent predictor of all-cause mortality (adjusted odds ratio 0.5, 95% confidence interval 0.2 to 1.2, p = 0.10). Target vessel revascularization was significantly lower in the DES group compared to the BMS group at 3 years (10.5% vs 21%, p = 0.001). DES use was an independent predictor of reduced target vessel revascularization (adjusted odds ratio 0.44, 95% confidence interval 0.25 to 0.77, p = 0.004). Late definite stent thrombosis occurring after 1 year occurred in 4 (2.5%) patients in the DES group compared to 6 (0.7%) in the BMS group (p = 0.05). DES use was an independent predictor of late stent thrombosis (adjusted odds ratio 8.6, 95% confidence interval 1.9 to 38, p = 0.004). In conclusion, this contemporary registry-based study of patients who underwent primary percutaneous coronary intervention for STEMI demonstrated improved revascularization rates without increased 3-year hazard of adverse clinical outcomes in DES-treated patients.