Abstract Background and objective Primary percutaneous coronary intervention (PPCI) is the gold standard for myocardial reperfusion in ST-segment elevation myocardial infarction (STEMI). Numerous studies have shown that thrombus aspiration can prevent distal embolization, reducing the risk of microvascular obstruction (MVO). Cardiac magnetic resonance (CMR) is considered the gold standard for evaluation of MVO. The aim of this study is to evaluate the efficacy of thrombus aspiration as adjunctive technique to primary PCI, in reducing incidence and extent of MVO in STEMI patients evaluated by CMR. Methods Ninety-three patients with heavy thrombus burden were enrolled in this study, sixty-five met our inclusion criteria. Aspiration thrombectomy followed by PCI was done for thirty-one patients (aspiration group) and conventional PCI, without aspiration thrombectomy, was done for thirty-four patients (conventional group). Primary end points were occurrence and extent of microvascular obstruction (MVO) evaluated by cardiac magnetic resonance (CMR). Results The incidence of microvascular obstruction (MVO) was significantly higher in conventional group (18 patients, 52.9%) when compared with aspiration group (7 patients, 22.6%) (p-value = 0.012). Moreover, significant difference existed between studied groups as regard MVO extent. In aspiration group, MVO extended to > 4 segments in 3 patients (9.7%) while in conventional group, MVO extended to > 4 segments in 13 patients (38.2%) (p-value = 0.012). Conclusion Aspiration thrombectomy as adjunctive technique to PCI in STEMI population maintains the integrity of coronary microvasculature and reduces both incidence and extent of MVO.