The endothelial to mesenchymal transition (EndMT) is the process by which endothelial cells lose a portion of their cellular features and obtain certain characteristics of mesenchymal cells, including loss of tight junctions, increased motility, and increased secretion of extracellular matrix proteins. EndMT is involved in cardiac development and a variety of diseases processes, such as vascular or tissue fibrosis and tumor. However, its role in specific diseases remains under debate. This review summarizes EndMT-related diseases, existing controversies, different types of EndMT, and molecules and signaling pathways associated with the process.