Invasive fungal infections cause significant morbidity and mortality in immunocompromised children. The prevalence of invasive aspergillosis (IA) is increasing as a reflection of the rising numbers of immunocompromised patients and the increasing use of aggressive immunosuppressive treatment regimes for hematologic malignancies and transplantation. IA is almost exclusively seen in severely immunocompromised or critically ill children, including those with the classic risk factors (particularly neutropenia, hematopoietic stem cell transplant or solid-organ transplantation, hematological malignancies, use of systemic immunosuppressive agents or cytotoxic therapies). Early treatment improves survival rates, but the diagnosis of aspergillosis remains difficult and, while IA has been relatively well-characterized in adults, far fewer studies have described optimal treatment for the pediatric population. This article reviews and compares the newer, less-invasive diagnostic techniques that are becoming available and focuses on the data specifically from pediatric trials regarding efficacy, safety and pharmacokinetics of the antifungals used for IA.