Aims Microvascular obstruction (MVO) is the underlying cause for the no-reflow phenomenon in ST-segment elevation myocardial infarction (STEMI). The association between MVO assessed by cardiac magnetic resonance imaging (CMR) and prognosis has not been convincingly demonstrated. We sought to determine the relationship between MVO assessed early after primary percutaneous coronary intervention (PCI) in STEMI and all-cause mortality, hospitalization for heart failure (HF), and reinfarction. Methods and results We performed a pooled analysis using individual patient data from seven randomized primary PCI trials in which MVO was assessed within 7 days after reperfusion by CMR using late gadolinium enhancement imaging (n = 1688). Clinical follow-up was performed for at least 6months after the index event. Median time to CMR after STEMI was 3 days [interquartile range (IQR) 2-4], and median duration of clinical follow-up was 365 days (IQR 188-374). Microvascular obstruction was present in 960 (56.9%) of patients, and median MVO (percent left ventricular myocardial mass) was 0.47% (IQR 0.00-2.54). A graded response was present between the extent of MVO (per 1.0% absolute increase) and subsequent mortality [Cox adjusted hazard ratio (HR) 1.14, 95% confidence interval (CI) 1.09-1.19, P < 0.0001] and hospitalization for HF (Cox adjusted HR 1.08, 95% CI 1.05-1.12, P < 0.0001). Microvascular obstruction remained significantly associated with all-cause mortality even after further adjustment for infarct size (Cox adjusted HR 1.09, 95% CI 1.01-1.17, P= 0.03). MVO was not significantly related to subsequent reinfarction (P = 0.29). Conclusions The presence and extent of MVO measured by CMR after primary PCI in STEMI are strongly associated with mortality and hospitalization for HF within 1 year.