The patient is a 12-year-old boy with acute mixed lineage leukemia (AMLL) and with a rare karyotype of trisomy 6. He was referred to our hospital with gingival swelling, bleeding at the conjunctiva and huge hepatosplenomegaly. Complete blood count revealed leukocytosis with 79% blasts, anemia and thrombocytopenia. Bone marrow examination revealed 82.5% blasts which were morphologically judged as M1 according to the French-American-British classification. Immunophenotyping of leukemic cells showed the presence of CD2, CD7, CD19 and CD13 antigens, suggesting the diagnosis of AMLL. Cytogenetic analysis revealed a single abnormal karyotype of 47,XY,+6,add(15)(q22) which was successfully detected by fluorescence in situ hybridization (FISH) with the probe mapping at the alpha-satellite region of chromosome 6. Although the patient was treated with several chemotherapy regimens, he could not achieve complete remission and he died of progressive disease 11 months after admission. Fluorescence in situ hybridization analysis was very informative in assessing the residual leukemic cells in interphase during his clinical course.