In systemic mastocytosis with associated clonal, hematological non-mast cell lineage disease (SM-AHNMD), mast cell infiltration of the bone marrow coexists with a hematologic neoplasm, usually of myeloid origin. Activating KIT gene mutations are universally present in these neoplastic mast cells. When SM is associated with AML, the leukemic cells commonly carry the t(8;21)(q22;q22) core binding factor translocation. The precise relationship between neoplastic mast cells and the leukemic clone has remained unclear. By target FISH analysis, we demonstrate t(8;21) in the bone marrow mast cells of a patient with systemic mastocytosis associated with t(8;21) AML, thus, proving the origin of these neoplastic mast cells from the leukemic clone. We also show that after successful allogeneic hematopoietic stem cell transplantation, these neoplastic bone marrow mast cells can persist without adverse consequences and gradually decline with time.