Most cases of leukemia show hTERT and WT1 gene overexpression. However, the role of these genes in the progression and monitoring of chronic myeloid leukemia (CML) has not been very well explored. Two hundred and eight patients diagnosed as having CML in chronic phase (CP), accelerated phase (AP), and blast crisis (BC) were studied. Real-time polymerase chain reaction (PCR) was performed for comparative quantification of BCR-ABL, hTERT, and WT1 gene expression. The expression levels of the three genes were compared among the three phases and seven imatinib-naive and -treated subgroups. Among the three major groups, the gene expression levels of hTERT (p < 0.01) and WT1 (p < 0.01) were significantly different. Freshly diagnosed, imatinib-responsive, and -unresponsive patients among these revealed interesting changes in hTERT and WT1 gene expression profiles, especially in 25 patients with CML in whom sequential samples were analyzed. Our results showed that hTERT and WT1 gene expression analyses provided relevant information for the understanding of disease progression and indicate their possible usefulness as surrogate markers for treatment monitoring.