Information on the effects of imatinib mesylate (IM) on the non-clonal bone marrow (BM) cell compartment is scanty. We have analyzed the gene expression profile of BM hematopoietic cells after IM therapy in 20 patients with chronic myeloid leukaemia (CML) in complete cytogenetic response (CCyR) and compared it with that of normal volunteer donors by oligonucleotide microarrays. In CCyR CML samples, IM induces a decrease in proliferation as well as increase in apoptosis and ubiquitination in residual non-clonal BM cells. In addition, IM diminishes cell-to-cell adhesion and downregulates the expression of the erythropoietin (EPO) receptor gene. The latter was confirmed by RT-PCR.