Patients with infant acute myeloid leukemia (AML) who carry a t(7;12)(q36;p13) translocation have been reported to have a poor clinical outcome. MNX1-ETV6 fusion transcripts (previously HLXB9-ETV6) were rarely detected in AML patients having t(7;12)(q36;p13). A 23-month-old girl with acute megakaryoblastic leukemia (AMKL) exhibited chromosome abnormalities, including add(7)(q22), and del(12)(p12p13). Southern blot analysis of bone marrow cells showed an ETV6 gene rearrangement. Reverse transcriptase-polymerase chain reaction (RT-PCR) followed by sequence analysis revealed the presence of an MNX1-ETV6 fusion gene. The patient responded well to chemotherapy, achieved complete remission, and at writing had been in complete remission for 60 months. The MNX1 expression by RT-PCR was significantly more frequent in Epstein-Barr virus-transformed B-cell lines derived from normal adult lymphocytes than in leukemic cell lines. This represents a novel case of an AMKL patient with MNX1-ETV6 fusion transcripts who had a good prognosis.