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Fungal endocarditis (FE) remains a rare infection, although its incidence is increasing because more neonates are in intensive care and more neonates are undergoing cardiac surgical procedures and central hyperalimentation (CHA). It rarely affects native valves and occurs most frequently in neonates as part of a disseminated fungal infection, in patients following cardiac surgery, or in those who develop an intracardiac thrombus or valvular injury due to a central venous catheter (CVC). Fungal endocarditis is often difficult to diagnose because the presentation may be nonspecific and the disease typically occurs in otherwise critically ill patients with confusing clinical pictures. Approximately one fourth of neonates and children with systemic candidal disease have a demonstrable cardiac lesion. Fungal infection usually occurs in a right-sided intracardiac thrombus or at the site of a valvular injury secondary to a CVC. Fungal endocarditis may also complicate intracardiac surgery or intrathoracic or systemic fungal infection, particularly in those at highest risk.