Infants with Down syndrome have increased incidences of transient abnormal myelopoiesis (TAM) and acute leukemia, which are usually associated with acute megakaryoblastic leukemia (AMKL). A 5-day-old girl with Down syndrome was diagnosed with TAM; 4 months later, acute leukemic transformation was suspected. Bone marrow (BM) examination was performed, and the infant was diagnosed with acute leukemia (80% blasts). Although BM aspirates showed the presence of megakaryocytic blasts with cytoplasmic blebs, flow cytometry analysis revealed that they were negative for cells with CD41a and CD61 immunophenotypes. Further analysis revealed that the megakaryocyte-related marker CD42a was positive in 57% of blasts. Morphologic and immunophenotypic features are required to establish the lineage of megakaryocytic blasts, which are necessary for diagnosing AMKL. As most cases of AMKL were positive for CD41 and/or CD61 markers, their presence was evaluated during routine analysis. In order to identify the immunophenotypic features of AMKL in an infant with Down syndrome, we performed additional flow cytometry for CD42a, one of the megakaryocytic markers, and were able to assist in the early diagnosis of AMKL, as well as to use CD42a as an effective follow-up marker.