Live imaging is extremely useful to characterize the dynamics of cellular events in vivo, yet it is limited in terms of spatial resolution. Correlative light and electron microscopy (CLEM) allows combining live confocal microscopy with electron microscopy (EM) for the characterization of biological samples at high temporal and spatial resolution. Here we describe a protocol allowing extracting endothelial cell ultrastructure after having imaged the same cell in its in vivo context through live confocal imaging during zebrafish embryonic development.