This Atlas provides an updated and practical overview of endocarditis with special attention to macroscopic and microscopic findings at autopsy. Although the decline of autopsies is a widespread phenomenon, we are strongly convinced that complex molecular-based studies have not overthrown autopsies but, conversely, they maintain an important and sometimes irreplaceable clinical, scientific, educational, epidemiological and public health value. This Atlas is the expression of a long-lasting cooperative experience of the Institute of Pathology and the Cardiovascular Department of the University Hospital of Trieste, Italy, that have been working together for years, with the aim at optimizing the diagnosis and treatment of cardiovascular disorders and at providing the best care to patients. The Institute of Pathology is an outstanding department, very active in clinical research and teaching with an exceptional experience in autopsy studies. The Cardiovascular Department of the University Hospital of Trieste is also a very active institution, with broad interests in many fields of cardiological sciences and is a reference center for cardiomyopathies, myocarditis and heart failure. The Department has a long liaison with the International Center for Genetic Engineering and Biotechnology and with the Center for Translational Cardiology, also in Trieste. These collaborations and exchange of ideas, data and programs represent a unique opportunity for students, residents, nurses and doctors to improve their knowledge and to develop original research projects in cardiovascular diseases. All the different complex problems related to endocarditis are analyzed in this the morphological substrates of this disease. This work has to be considered a useful educational scientific support for students, nurses and physicians, cardiologists, specialists in infective diseases and cardiac surgeons who want to multidisciplinary team approach.