Objective To explore the clinical value of chromosome analysis and quantification of bcr-abl fusion gene transcripts in patients with chronic myeloid leukemia(CML). Methods The bone marrow cells were collected from 17 CML patients on their first visit and before every treatment. The chromosomes were obtained after short-time of cell culture and then analyzed under microscope after G-banding and R-banding. At the same time transcripts of bcr/abl gene was quantified by real time fluorescence quantification RT-PCR. Track observations for 9 patients were performed. Results Ph chromosomes and bcr/abl gene transcripts were detected in all patients, but great variation existed among these patients in the level of bcr/abl gene. After routine treatment, the levels of bcr/abl gene in 4 patients were in stable status with slight increase or decrease and no additional abnormal chromosomes appeared. The level of bcr/abl gene increased averagely 9. 06 times in 3 patients who experienced deterioration from chronic phase to acute phase and additional abnormal chromosomes appeared in all the 3 patients. In 2 patients who were given allogeneic bone marrow transplantation, the expression level of bcr/abl gene changed with the clinical treatment. The patients with the same variance of bcr/abl gene expression and different chromosome analysis results responded differently to chemotherapy and the prognosis was also different. Conclusions Chromosome analysis combined with quantification of bcr/abl gene provide a good way to display the status of CML patients and was highly correlated to the development of the disease, and was significant for diagnosis of CML and evaluation of leukemia cell load, as well as for treatment and prognosis.