Endothelial colony-forming cells (ECFCs) are known to increase after acute myocardial infarction (AMI). We examined whether the presence of ECFCs is associated with preserved microvascular integrity in the myocardium at risk by reducing microvascular obstruction (MVO). We enrolled 88 patients with a first ST elevation AMI. ECFC colonies and circulating progenitor cells were characterized at admission. MVO was evaluated at 5 days and infarct size at 5 days and at 6-month follow-up by magnetic resonance imaging. ECFC colonies were detected in 40 patients (ECFC^pos patients). At 5 days, MVO was of greater magnitude in ECFC^neg versus ECFC^pos patients (7.7 ± 5.3 vs. 3.2 ± 5%, p = 0.0002). At 6 months, in ECFC^pos patients, there was a greater reduction in infarct size (−32.4 ± 33 vs. −12.8 ± 24%; p = 0.003) and a significant improvement in left ventricular (LV) volumes and ejection fraction. Level of circulating CD34+/VEGF-R2+ cells was correlated with the number of ECFC colonies (r = 0.54, p < 0.001) and relative change in infarct size (r = 0.71, p < 0.0001). The results showed that the presence of ECFC colonies is associated with reduced MVO after AMI, leading to reduced infarct size and less LV remodelling and can be considered a marker of preserved microvascular integrity in AMI patients.