Data regarding clinical efficacy of thrombectomy in patients with acute myocardial infarction (AMI) have been still limited in Japan. Using the AMI-Kyoto Multi-Center Risk Study database, the clinical background characteristics, angiographic findings, primary percutaneous coronary intervention (PCI) results and in-hospital prognoses were retrospectively compared between AMI patients with totally occluded infarct-related artery (IRA) (TIMI flow grade 0) undergoing thrombus aspiration during primary PCI (with-aspiration patients, n = 568) and those without thrombus aspiration (without-aspiration patients, n = 266). The with-aspiration patients were more likely to have higher TIMI grade in the IRA immediately after primary PCI, and had a lower in-hospital mortality rate than the without-aspiration patients. According to a multivariate analysis, thrombectomy as well as stent usage was found to be independent predictor of final TIMI flow grade ≥2 in the IRA, and the final TIMI flow grade ≥2 in the IRA was found to be an independent factor for in-hospital survival. These results suggest that among real-world, unselected Japanese AMI patients with totally occluded IRA on initial coronary angiography, thrombus aspiration is an effective adjunctive therapy during primary PCI to improve final epicardial coronary flow in the IRA, which might lead to better in-hospital prognosis.