The translocation t(16;21)(p11;q22) is rare, occurs with an incidence of 1%, in acute myeloid leukemia (AML), forming TLS/FUS-ERG fusion transcript, and it is known to cause the hemophagocytosis and vacuolation of leukemic cells. As previously reported cases numbered less than 60, we aimed to identify the clinical and genetic aspects of AML with t(16;21). Among 1,277 patients diagnosed with de novo and secondary AML, 12 AML patients with t(16;21) were retrospectively evaluated (0.94%, 12/1,277). AML with t(16;21) expressed CD56 with a median value of 45% (7.8-87%), and the rate of hemophagocytosis plus vacuolation of leukemic cells was 2.9% (2.0-9.0%). CD56 antigen expression showed a correlation with the total rate of hemophagocytosis plus vacuolation, with a correlation coefficient of 0.663 (P = 0.019). AML with t(16;21) expressed CD13, CD33, CD34, CD117, CD56, HLA-DR, and cytoplasmic myeloperoxidase. RUNX1, which regulates a gene for hematopoiesis, is frequently mutated in AML and, in this study, one out of three patients showed the mutation R174Q in RUNX1. All of these 3 patients showed the fusion transcript TLS/FUS-ERG, which was detected by multiplex or nested PCR. AML with t(16;21) showed a very low rate of complete remission after induction chemotherapy (8.3%), and high relapse (75%) and mortality (75%) rates. AML with t(16;21) exhibited a distinct morphology with frequent CD56 expression and a poor prognosis.