The concept of antisense-mediated gene inhibition has emerged as a potentially powerful alternative or adjunct to conventional cancer chemotherapy. The discovery that synthetic fragments of DNA can inhibit the transcription and/or translation of selected genes in a sequence-specific manner initially opened up a new mechanism for analyzing gene function, then launched a new field of drug development The prominence of the Philadelphia chromosome has placed BCR-ABL, the neogene and its messenger RNA in the forefront among potential targets of antisense CML therapy. The present work aimed to expose CML progenitors to antisense ODN targeting one or the other of the two common BCR-ABL junctions, termed b2a3 and b3a2. This was followed by the assessment of colony formation by Ph+ve CML progenitors. This may help to demonstrate the general usefulness of antisense oligodeoxynucleotides for the inhibition of the BCR-ABL chimeric gene created by the unique chromosomal abnormality of CML. Cases with accelerated CML showed significantly higher colony count in the control culture (i.e without AS-ODN) in comparison to either de novo CML or CML under treatment. TAT ODN and b3a2 AS-ODN caused non-specific inhibition of proliferation of Ph-positive cells and the inhibition of the colony formation was significantly more evident in cases with either de novo CML or CML under treatment. b2a2 AS-ODN caused a remarkable decrease in the colony count in patients with de novo CML and CML patients under treatment. Colony count after pre-incubation of MNCs of de-novo CML patients with either b2a2, b3a2 AS-ODN or TAT ODN revealed a highly significant reduction of the colony count when b2a2 AS-ODN was used. This indicates that b2a2 is the characteristic chimeric gene in the studied cases. Similar results were found in CML patients under treatment. This may raise the possibility that b2a2 is the common chimeric BCR-ABL gene in Egyptian CML patients. The inhibition of colony formation in semisolid culture in the presence of BCR-ABL junction specific antisense ODN demonstrated in the present work proves that the growth of CML progenitor cells is dependent on BCR-ABL expression. CML cases in the accelerated phase did not show any significant inhibition in the in-vitro colony formation after the pre-incubation with AS-ODN. In the present work, it was not clear why there was no complete inhibition of colony formation when the specific AS-ODN was used in de novo-CML or in CML under treatment. This partial inhibitory effect of b2a2 AS-ODN likely reflects the insufficient uptake of ODNs by leukemic cells in vitro. Also the inevitable presence of myeloid cells of intermediate stage of differentiation in the mononuclear fraction can decrease the amount of ODNs available to clonogenic cells, thereby reducing the response to ODNs. Thus the use of CD34+ cells may increase the sensitivity and specificity of AS-ODN treatment. In conclusion, CML is currently incurable and eventually end by blastic crisis, thus nucleic-acid therapeutics appears to be highly desirable. However, there are still problems facing the gene therapy and potential strategies for overcoming them are highly required.