Acute and late stent malapposition (SM) after bare-metal stents (BMS) and sirolimus-eluting stents (SES) in ST-segment elevation myocardial infarction patients were studied. Stent thrombosis may be caused by SM after primary percutaneous coronary intervention in ST-segment elevation myocardial infarction patients. Post-procedure and follow-up intravascular ultrasound data were available in 184 out of 310 patients (60%; 104 SES, 80 BMS) included in the MISSION! Intervention Study. To determine the contribution of remodeling and changes in plaque burden to the change in lumen cross-sectional area (CSA) at SM sites, the change in lumen CSA (follow-up minus post-lumen CSA) was related to the change in external elastic membrane CSA (remodeling) and change in plaque and media CSA (plaque burden). Acute SM was found in 38.5% SES patients and 33.8% BMS patients (p = 0.51), late SM in 37.5% SES patients and 12.5% BMS patients (p < 0.001). Acquired SM was found in 25.0% SES patients and 5.0% BMS patients (p < 0.001). Predictors of acute SM were reference diameter (SES: odds ratio [OR] 3.49, 95% confidence interval [CI] 1.29 to 9.43; BMS: OR 28.8, 95% CI 4.25 to 94.5) and balloon pressure (BMS: OR 0.74, 95% CI 0.58 to 0.94). Predictors of late SM were diabetes mellitus (SES: OR 0.16, 95% CI 0.02 to 1.35), reference diameter (BMS: OR 19.2, 95% CI 2.64 to 139.7), and maximum balloon pressure (BMS: OR 0.74, 95% CI 0.55 to 1.00). Change in lumen CSA was related to change in external elastic membrane CSA (R = 0.73, 95% CI 0.62 to 0.84) after SES implantation and to change in plaque and media CSA (R = -0.62, 95% CI -0.77 to -0.46) after BMS implantation. After SES implantation, acquired SM was caused by positive remodeling in 84% and plaque reduction in 16% of patients. Acute SM was common after SES and BMS stent implantation in ST-segment elevation myocardial infarction patients. After SES implantation, late acquired SM is common and generally caused by positive remodeling.