Gaining knowledge on the biochemical profile of primary endothelial cells on a subcellular level can contribute to better understanding of cardiovascular disease. In this work, primary cardiac microvascular endothelial cells (CMECs) isolated from the mouse heart and murine H5V endothelial cell line were characterized with the use of a Raman imaging technique. Primary CMECs displayed a distinct Raman-based biochemical phenotype as compared with other cells isolated from the heart and were characterized by a low lipid content. In contrast to the murine H5V endothelial cell line, CMECs did not display lipid droplets (LDs) in the cytoplasm, while the former have many low-unsaturated LDs. In conclusion, Raman imaging is a fast and efficient tool to analyse single coronary endothelial cells in a non-invasive manner that can prove useful to characterize biochemical changes in a single isolated primary endothelial cell from a diseased heart.