Chemotherapy, while undeniably effective in controlling or eradicating a variety of neoplasms, is also accompanied by a number of toxicities. Foremost among these is neutropenia, which places the pediatric cancer patient at risk for serious fungal infections. The fungal organisms most commonly responsible for infection in neutropenic children are Candida, Aspergillus, Mucor, and the Phycomycetes. Common sites of infection include the oral cavity, sinuses, lung, and bloodstream. Recently, candidal infection of the liver was recognized as a growing problem. Diagnosis of deep-seated fungal infections, such as pneumonia and hepatic candidiasis, is extremely difficult, often requiring open-lung or liver biopsy, which a patient's hematologic status may not permit. Because early treatment significantly improves prognosis, empirical antifungal therapy may be indicated in selected patients. Amphotericin B is currently the antifungal agent of choice against most fungal organisms. Antifungal efficacy studies based on animal models of disseminated candidal infection suggest that amphotericin B combined with 5-fluorocytosine (5-FC) is more effective than amphotericin B alone against most deep-seated Candida infections. The investigational drug, fluconazole, appears as effective as amphotericin B plus 5-FC in the prevention and early treatment of disseminated candidiasis, and clinical trials to assess this potentially important role for the new antifungal agent are now being initiated.