CML is a prototype of a disease in which the molecular oncogenesis is known, caused by the Philadelphia chromosome. The introduction of antisense oligodeoxynucleotides (AS-ODNs) against the transcribted mRNA of b3a2 and b2a2 breakpoints leads to suppression of translation of the abnormal p210 tyrosine kinase protein. Comparing b2a2 AS-ODNs inhibition ratio to both b3a2 and TAT AS-ODNs inhibition ratio showed a highly significant statistical difference. Also there was a significant negative statistical correlation between AS-ODNs inhibition ratios and both basophil percent and LAP score in chronic phase CML thus AS-ODNs can be used to purge autologous stem cells to reduce malignant cells before its transplantation in chronic phase CML.