Chronic Myeloid Leukaemia (CML) is a hematopoietic stem cell disease, the hallmark of which is the BCR-ABL protein tyrosine kinase (PTK). Without intervention the disease progresses from a benign chronic phase to a rapidly fatal blast crisis. To identify the molecular mechanisms underlying disease progression we employed 2-dimensional gel electrophoresis on a model we have previously described using the expression of a conditional mutant of Bcr-Abl PTK in a multipotent stem cell line, FDCP-Mix. Long-term exposure of FDCP-Mix cells to Bcr-Abl mimics disease progression in CML. Four major differences were observed as a consequence of long-term exposure to the Bcr-Abl PTK, compared to cells exposed short-term. The proteins were identified using MALDI-ToF MS generated peptide mass fingerprint data and liquid chromatography-tandem MS generated sequence information. Leukotriene A4 hydrolase, an enzyme known to be deregulated in CML, was found to be upregulated. Annexin VI, vacuolar ATP synthase catalytic subunit A and mortalin were found to be downregulated. PolyA PCR cDNA analysis showed there was no correlation between the protein expression changes and mRNA levels. Western blot analysis also indicated no change in the levels of mortalin or leukotriene A4 hydrolase, indicating post-translational events may modify protein content of the specific spots. Leukotriene B4 levels (product of LTA4H) were, however, reduced in cells exposed long term to Bcr-Abl activity. This study demonstrates the potential of proteomic analysis to define novel effects of oncogenes.