Endocarditis is an infection of a heart valve or the inner lining of the heart (the endocardium). Infection can damage or destroy the heart valves and damage the heart.Endocarditis usually occurs in patients with congenital (i.e., present at birth) or acquired heart conditions (e.g., atrial septal defects, valve disease). Although several different organisms can cause endocarditis, it is usually caused by bacteria.In most cases, it develops when normal bacteria on the skin or in the respiratory, gastrointestinal, or urinary tract enter the bloodstream and lodge within a damaged heart valve or abnormal heart tissue.lthough several different organisms can cause endocarditis, it is usually caused by bacteria. In most cases, it develops when normal bacteria on the skin or in the respiratory, gastrointestinal, or urinary tract enter the bloodstream and lodge within a damaged heart valve or abnormal heart tissue.