The endocardium is the innermost layer of tissue that lines the chambers of the heart.Its cells are embryologically and biologically similar to the endothelial cells that line blood vessels. The endocardium also provides protection to the valves and heart chambers.ecently, it has become evident that the endocardium, which is primarily made up of endothelial cells, controls myocardial function. This modulating role is separate from the homeometric and heterometric regulatory mechanisms that control myocardial contractility.