This study was aimed to investigate the sensitivity and clinical application value of interphase-dual-color and dual-fusion fluorescence in situ hybridization (DD-FISH). The minimal residual disease (MRD) in 19 patients with chronic myelogenous leukemia (CML) after allogeneic hematopoietic stem cell transplantation (allo-HSCT) was detected by DD-FISH, and the detected results were compared with those of conventional cytogenetics (CC) and reverse transcription-polymerase chain reaction (RT-PCR). The samples were collected from bone marrow or peripheral blood or smears of bone marrow. The results indicated that 14 out of 19 patients achieved and maintained continuous complete molecular remission after transplantation. In these patients, CC assay displayed normal donor karyotype, result of RT-PCR was negative, complete donor chimerism was detected after 2 months of transplantation, result of DD-FISH was negative, average time of the follow-up survey was 11.25 months, MRD did not increase. Results of CC and RT-PCR in 1 patient showed negative, while FISH of sex chromosome showed mixed chimerism, result of DD-FISH was positive, MRD did not increase, no therapy was given for this patient, clinical state of patient was stable. Three patients with hematological relapse demonstrated obvious increase of MRD detected by DD-FISH and sex FISH, result of RT-PCR was found positive in them, but the abnormal result of CC was observed only in 1 patient. After donor lymphocyte infusion and imatinib mesylate treatment, these 3 patients achieved cytogenetic remission again, results of DD-FISH, CC and PCR were negative in them. DD-FISH, CC and PCR in bone marrow and peripheral blood from one patient with extramedullary relapse revealed negative results, and the complete chimerism was found in this patient. It is concluded that interphase-dual-color and dual-fusion fluorescence in situ hybridization is a more reliably sensitive and practicable method for monitoring MRD in patients with CML after allo-HSCT, and can be used in detection of chromosome sample and blood or bone marrow smears. Dynamic detection of bcr/abl fusion gene level by FISH may predict disease changes and guide individual therapy.