Applications of flow cytometry in pediatric cancers have expanded substantially in recent years. In acute leukemias, the commonest childhood cancer, flow cytometry can now define complex antigenic profiles that are associated with specific cytogenetic/molecular defects and can also directly identify BCR-ABL fusion protein. Flow cytometry based scoring system has been described for diagnosis of myelodysplastic syndromes. In solid tumors, flow cytometry was previously used mainly to determine DNA content for prognosis; however, recent studies in children with neuroblastoma and Ewing sarcoma have identified its diagnostic utility. In this review, we will discuss the current and future applications of flow cytometry in pediatric hematology-oncology. Pediatr Blood Cancer 2011;57:18–29. © 2011 Wiley-Liss, Inc.