AML1-ETO is a leukemogenic fusion protein generated by chromosomal translocation t(8; 21) (q22; q22), one of the most frequent chromosomal abnormalities in acute myeloid leukemia. The fusion protein has been shown to present dichotomous functions on leukemic cells: growth arrest versus differentiation block. However, their precise molecular mechanisms are not completely clear. In this work, we try to explore potential AML1-ETO-targeted proteins through comparing two-dimensional electrophoresis (2DE)-based global protein expression profiles of leukemic U937 cells with and without inducible expression of AML1-ETO. As a result, we identified 14 unique proteins deregulated in AML1-ETO-carrying leukemic cells, including 3 up-regulated such as hairy and enhancer of split 5 (HES5) and 11 down-regulated such as MAT1 (menage a trois-1) and mitogen-activated protein kinase organizer 1 (MORG1). These proteins were widely involved in stem cell maintenance, cell cycle, signal transduction and transcription. The further investigation on their roles in leukemic cells will uncover new clues to understanding leukemogenic effects of AML1-ETO fusion protein.