Restoring blood flow to ischemic but viable myocardium and reducing infarct size constitute the goals of reperfusion therapy with fibrinolytic drugs or primary percutaneous intervention in patients with ST-segment elevation myocardial infarction (STEMI). However, in a sizable proportion of patients, this intervention gains to reopen the obstructed epicardial coronary artery but does not achieve myocardial reperfusion because of coronary microvascular obstruction phenomenon (CMVO). In the last years, consistent evidence has pointed out how CMVO has a negative impact on outcome in patients with acute STEMI. Of note, most of the trials in this setting, mainly targeting reperfusion damage, have failed to show beneficial effects. In this article we provide a revision of mechanisms, diagnosis and prognosis of CMVO in acute STEMI, also pointing out the need of an integrated approach in order to prevent and treat CMVO in the different time windows of the acute event.