Objective: Primary percutaneous coronary intervention is the standard treatment for ST-segment elevation myocardial infarction. Although myocardial and epicardial perfusion is usually achieved with primary percutaneous coronary intervention, infarct-related arterial thrombus burden negatively affects the procedural success and clinical outcomes of primary percutaneous coronary intervention. Therefore, we aimed to investigate the association between thrombus burden (calculated before and after initial flow) and clinical consequences in patients with ST-segment elevation myocardial infarction. Materials and Methods: This study retrospectively enrolled 1376 patients who had ST-segment elevation myocardial infarction between May 2012 and November 2015. Patients who had only undergone balloon angioplasty and emergency coronary artery bypass grafting were not included in the study. Data regarding the initial clinical and demographic features of the patients were obtained from their hospital records. Thrombus burden was calculated using baseline and final (after wire inflation or small balloon dilatation) thrombolysis in myocardial infarction thrombus grades. The endpoints of the study were defined as no-reflow development after primary percutaneous coronary intervention and 1-year all-cause mortality. Statistical significance was defined as P < .05. Results: No-reflow was detected in 169 patients (12.3%). The calculated basal thrombus burden was significantly associated with post-procedural no-reflow (P < .001). No-reflow was also associated with advanced age (P < .001), longer pain-to-door time (P < .001), and increased blood glucose levels (P = .032). The calculated final thrombus burden was related to 1-year all-cause mortality (P = .047). One-year all-cause mortality was also associated with advanced age (P < .001), high Killip scores (P = .003), increased white blood cell counts (P = .001), and low estimated glomerular filtration rates (P < .001). Conclusion: Basal thrombus burden was associated with no-reflow, and final thrombus burden was associated with 1-year all-cause mortality. The calculation of thrombus burden before and after initial flow may help to predict clinical outcomes.