The BCR-ABL fusion gene arises as a result of a reciprocal translocation between chromosomes 9 and 22, resulting in the so-called Philadelphia (Ph) chromosome (a minute chromosome 22), which is found in 95% of cases of chronic myeloid leukemia (CML) (1 ). A variable sequence length of the BCR gene at 22q11 fuses with ABL at 9q34 and encodes the constitutively active BCR-ABL protein tyrosine kinase (reviewed in refs. 2 and 3 ). Data from animal models have demonstrated that this protein is capable of inducing a CML-like disease in mice, indicating its central importance in the pathogenesis of CML as well as other leukemias (viz. 20% of adult acute lymphoblastic leukemia and the rare chronic neutrophilic leukemia). Detection of the BCR-ABL translocation is, therefore, important from both clinical and research perspectives. BCR-ABL positive cells do not have a reliable immunophenotypic marker to distinguish them from their normal counterparts; therefore, proof of their clonal origin requires either reverse transcriptase-polymerase chain reaction (RT-PCR), conventional G-banding of metaphase (MP) spreads, or direct visualization of the BCR-ABL translocation by fluorescence in situ hybridization (FISH). The advantages of FISH over G-banding include applicability to interphase (IP) cells, greater sensitivity (as many more cells can be analyzed), and ability to detect masked translocations. This has led to its use in the clinical setting for monitoring response to therapy, by quantifying the size of the BCR-ABL clone on either bone marrow (BM) or peripheral blood (PB) specimens.