Mycotic infections have become an increasingly common problem in immunosuppressed pediatric patients. The management of fungal infections requires not only the recognition of the potential for infection, but also of the types of organisms that can cause infection. The identification of the organ system(s) affected is important in directing therapy. The immature immune system of neonates is partially responsible for some specific diseases and unique management problems. These infants are increasingly stressed to degrees not previously seen in intensive care nurseries and may be on long-term antibiotic therapy for other illnesses. Chemotherapy for malignancy, bone marrow transplants, trauma, and chronic illness increase the risk of immunocompromise and systemic fungal infections. The frequent use of long-term intravascular catheters contributes to the potential for fungal infection in the pediatric population. Therapy now includes administration of topical and/or parenteral antifungal agents and supportive care to the patients. New therapies may well include more potent and safer antifungal agents as well as new ways to enhance the immune response in immunosuppressed patients.