Embryonal tumours constitute the largest group of malignant pediatric brain tumours. Their origin and histological classification is debated. Diagnosis is controversial and patients' response to therapy on the basis of morphologic appearance alone, is difficult to predict. Therefore accurate clinical staging remains a critical component of clinical management. In recent years real progress has been made in our understanding of the molecular genetic abnormalities that govern the initiation and/or progression of embryonal tumours. This review is focused on the principal molecular genetic abnormalities so far identified in embryonal brain tumours and discusses their possible biological and clinical applications in developing a molecular risk staging system which hopefully will lead to the molecular targeted therapies, curative non-toxic treatment for all children.