We assessed the effect of thrombus aspiration (TA) during percutaneous coronary intervention (PCI) on in-hospital and 3-year mortality in consecutive non-ST segment elevation myocardial infarction (n = 189) and unstable angina pectoris (n = 148) patients (n = 337) between 2011 and 2016. In total, 153 patients (45.4%) underwent TA. The number of patients with postoperative thrombolysis in terms of myocardial infarction grade 3 blood flow (P < .001) and myocardial blush grade 3 (P < .001) were significantly higher in all TA groups. At 6-, 12- and 24-month post-PCI, the mean left ventricular ejection fraction was significantly higher in the all TA groups versus the stand alone PCI group (P < .001). Thrombus aspiration was associated with a significant improvement both in epicardial flow, myocardial perfusion and left ventricular ejection fraction. Thrombus aspiration during PCI in all acute coronary syndrome (except ST segment elevation) patients was associated with better survival compared with stand alone PCI group at 3-year follow-up (P = .019).