Fungal infections have emerged as one of the most significant complications of antineoplastic therapy and marrow transplantation in children. Morbidity and mortality associated with fungal infections are high. Recent trends indicate that the incidence and spectrum of fungal infections are increasing, partly because of the increase in the number of children receiving intensive chemotherapy and marrow transplantation, but also because of the successful management of bacterial and viral infections. Though many factors may contribute to risk for developing a fungal infection, prolonged neutropenia is the most important. Until recently, options for antifungal therapy were limited. Advances include less toxic formulations of amphotericin B and an expanding armamentarium of azoles as well as new antifungal compounds. This review addresses the therapeutic options available for treatment of fungal infections in immunocompromised children.