Rapid and accurate detection of BCR-ABL fusion proteins is vital for the diagnosis and classification of leukemias, especially chronic myeloid leukemia (CML) and acute lymphoblastic leukemia (ALL). Recently, the cytometric bead array (CBA) system has been used to identify BCR-ABL proteins in leukemic cell lysates. To evaluate the accuracy of this new technique, we tested 70 patients with hematological diseases using the CBA system, cytogenetic analysis, fluorescence in situ hybridization (FISH) and real-time quantitative polymerase chain reaction (RQ-PCR). Most of the results obtained by the CBA system were concordant with those by cytogenetic analysis, FISH and RQ-PCR. In the CBA system, dilution experiments with positive control samples revealed sensitivities of at least 1%. The statistical analysis revealed that the mean fluorescence intensity (MFI) values of the BCR-ABL fusion proteins from mononuclear cells (MNCs) were higher than those from WBC or BM samples. The MFI values of cells were not dramatically reduced after 24 hours of storage at room temperature. The CBA technique detected all types of BCR-ABL proteins in leukemic cells with high specificity and sensitivity. Therefore, CBAs will contribute to the fast and easy diagnosis of leukemias, the classification of leukemias and the monitoring of minimal residual disease (MRD).