Primitive neuroectodermal tumors constitute a large class of pediatric brain tumors. Despite notable recent advances in improving treatment and survival, the pathogenesis and the molecular genetic bases of these malignancies remain poorly understood. Combined cytogenetic and molecular genetic approaches have been used to identify genomic alterations in different histologic tumor types. Translation of these advances from basic science to clinical application is currently underway. Goals for the future include the development of more efficacious treatment strategies while simultaneously lessening toxicity. The most important cytogenetic and molecular genetic abnormalities documented to date together with their potential prognostic significance are reviewed.