Invasive fungal infections have emerged as important causes of morbidity and mortality in profoundly immunocompromised children including cancer, transplant and intensive care unit patients. Present treatment strategies for these infections are limited by toxicity, drug interactions and expense. In order to overcome these limitations, new antifungal compounds are being developed, which may improve the therapeutic armamentarium for prevention and treatment of invasive mycoses in high-risk children. This article summarizes the clinical pharmacology of established and newly developed antifungal agents, including new triazoles and echinocandins in pediatric age groups.