This study was purposed to set up real-time quantitative RT-PCR technique and to measure leukemia fusion gene transcripts in patients with chronic myeloid leukemia (CML), acute lymphoblastic leukemia (ALL) and acute promyelocytic leukemia (APL). All plasmids containing the target gene sequences were constructed to establish the standard curves. A TaqMan based real-time quantitative RT-PCR was performed to measure aberrant fusion gene transcripts in 130 samples of peripheral blood (PB) or bone marrow (BM) from 49 patients with leukemia. The results showd that the BCR-ABL(P210) transcripts were detected in 28 (82.4%) out of 34 CML patients (the ratios of BCR-ABL(P210)/ABL varied from 0.01 to 3.19) and also in 2 (33.3%) out of 6 ALL patients. The BCR-ABL(P190) transcripts were detected in 2 (33.3%) out of 6 ALL patients. The BCR-ABL(P210) and BCR-ABL(P190) transcripts were both detected in 1 (2.9%) CML patients. The PML/RARalpha transcripts were detected in 7 (77.8%) out of 9 APL patients (the ratio of PML-RARa/ABL varied from 0.0014 to 3.199). The relative frequency of both bcr1 and bcr3 was 42.9%, while that of bcr2 was 14.3%. The transcript level of aberrant fusion gene varied from the clinical situation of patient. It is concluded that real-time quantitative PCR is a reliable, innovative and promising technology with high sensitivity and specialty. It has potential clinical value for defining diagnosis, typing tumor, selecting treatment, measuring the tumor load, monitoring fusion gene expression level and evaluating therapeutic strategies, which is worthy to be popularized.