The stable transfection of the canine CD34(-) multipotent cell line DO64 with retroviral constructs containing the cDNA for the canine major histocompatibility complex (MHC) class II DR genes led to the cell clone DO64#14, which is characterized by malignant transformation and tumor growth in nonobese diabetic/severe combined immunodeficient (NOD/SCID) mice. The additional expression of p27(kip-1) in the transformed cell clone partially reversed the malignant phenotype. Because several proteins associated with lipid rafts are involved in signal transduction and because changes of lipid raft composition are linked to the pathogenesis of leukemias, raft-associated proteins in DO64 cells and the deduced transformed cell clones were compared using a proteomic approach. Raft-associated proteins were separated by two-dimensional electrophoresis and identified by MALDI-TOF-MS. Here we show that the stem cell line DO64 and the deduced cell clones can clearly be distinguished by differences in the expression of a number of raft-associated proteins, namely caveolin-1, flotillin- 1, vimentin, galectin-3, and glyceraldehyde-3-phosphate dehydrogenase. All identified proteins play an important role in cellular functions and may therefore participate in raft-mediated leukemic transformation. Therefore, our study suggests that the analysis of lipid raft protein composition may be useful for the identification of molecular markers of the transformation process.