Microvascular obstruction (MVO) is a strong independent predictor of left ventricular remodelling and mortality following ST-segment elevation myocardial infarction (STEMI). Microvascular obstruction can be identified at angiography or with gadolinium-enhanced cardiac MRI (CMR). First-pass perfusion CMR also allows a novel quantitative evaluation of myocardial blood flow (MBF) that might provide superior predictive data in the assessment of MVO. We sought to compare angiographic and CMR derived methodologies in the assessment of MVO to determine the optimal methodology that best predicts the surrogate outcome marker of left ventricular function post STEMI. Following primary-PCI angiographic assessment of 'no-reflow' with TIMI myocardial perfusion grade (TMPG) and myocardial blush grade (MBG) were documented. Assessment of CMR derived MVO was assessed on day 3, with MVO on first-pass perfusion imaging termed 'early MVO' and on late gadolinium enhancement, 'late MVO'. Furthermore on the same day 3 CMR scan, myocardial blood flow in the infarct region was quantified at adenosine stress and rest utilizing standard perfusion imaging sequences. Assessment of remodelling, structure and function was undertaken via standard CMR imaging assessment on day 90 post-STEMI and was used as the surrogate marker for long term clinical outcome. Forty patients (age 59 ± 12 years, 84% males) were appraised. Late MVO had the strongest correlation with LVEF at 90 days compared to the CMR parameters of early MVO, stress infarct region MBF and rest infarct region MBF (r = -0.754, r = -0.588, r = 0.595 and r = 0.345 respectively). Of the angiographic parameters used to assess MVO, TMPG had the strongest relationship with MVO when assessed via CMR. Myocardial blush grade however showed no relationship to CMR derived assessment of MVO. On multivariate analysis, of all angiographic and CMR variables, late MVO was the strongest predictor of LVEF at 90 days (p = 0.004). Cardiac magnetic resonance imaging derived assessment of microvascular obstruction on late gadolinium enhancement strongly predicts left ventricular function following STEMI at 90 days.