The prevalence of invasive fungal infections is increasing and the infections are becoming a major problem in immunocompromised children and neonates. Fortunately, there has been a recent surge in the development of new antifungal agents. Caspofungin, the first licensed echinocandin, is a novel class of antifungal and is approved for use in children 3 months of age or older for the treatment of invasive candidiasis, salvage therapy for invasive aspergillosis and as empirical therapy for febrile neutropenia. This article reviews the published data on the use of caspofungin in immunocompromised children and neonates with invasive fungal infections.