Coronary arteries are covered by a thin layer of endothelial cells (ECs). Impairment of ECs is at the origin of coronary atherosclerosis and its clinical manifestations. However, the study of ECs in humans remains elusive because of a lack of an imaging tool with sufficient resolution. We have developed a light-based 1-µm-resolution microscopic imaging technology termed micro-optical coherence tomography (µOCT) that can be implemented in a coronary catheter. In this study, we investigated the capability of µOCT to visualize EC morphology. We stripped the endothelium from 36 fresh swine coronary segments with cyanoacrylate glue. Histology showed that the stripping procedure successfully removed ECs from the swine coronary arteries. Coronary segments were then imaged in 3D with µOCT, and were processed for histology and scanning electron microscopy (SEM). µOCT images of stripped vs. intact sites were volume rendered in 3D and visually compared. 3D-µOCT allowed visualization of EC pavementing on intact artery surfaces that was strongly correlated to that seen by SEM. EC pavementing disappeared, and surface roughness calculated by computed root mean squared error diminished significantly at the sites with stripped EC compared with intact sites. µOCT was also utilized in human cadaver coronary arteries, showing its capability of identifying EC morphology of human coronary plaque harboring leukocyte adhesion, EC stent strut tissue coverage, and lack of ECs at lesions with necrotic core or superficial nodular calcifications. In conclusion, µOCT enables EC visualization in coronary arteries, suggesting that it could be useful in patients with coronary artery disease to better understand the role of ECs in the pathogenesis of coronary artery disease.