Endocarditis is usually caused by an infection with bacteria, fungi or other germs. The germs enter the bloodstream and travel to the heart. In the heart, they attach to damaged heart valves or damaged heart tissue. Usually, the body's immune system destroys any harmful bacteria that enter the bloodstream. However, bacteria on the skin or in the mouth, throat or gut (intestines) may enter the bloodstream and cause endocarditis under the right circumstances.