We report cytogenetic, fluorescence in situ hybridization (FISH), and molecular analysis in a case of Ph-negative chronic myelogenous leukemia patient with ABL/BCR fusion gene on chromosome 9 and a disparate FISH signal pattern using two commercially available bcr/abl probes (Vysis, Inc. and Oncor, Inc.). Cytogenetic analysis revealed a 46,XX normal female karyotype. FISH studies using Vysis LSI bcr/abl probe in interphase cells demonstrated a BCR/ABL fusion pattern, similar to that of m-BCR/ABL fusion found in acute lymphoblastic leukemia. However, examination of metaphases revealed the ABL/BCR fusion signal on one of the chromosomes 9, an ABL signal on the other chromosome 9, and two BCR signals of different sizes on each of the chromosomes 22. Subsequently, a FISH study with the Oncor major (M)-bcr/abl translocation probe confirmed the ABL/BCR fusion signal on chromosome 9 in addition to an ABL signal and a BCR signal located on chromosomes 9 and 22, respectively. Molecular studies (RT-PCR) revealed a rearrangement of the M-BCR region and expression of a chimeric bcr/abl mRNA of b3a2 configuration. This case suggests that it is imperative to have a full understanding of both the capabilities and the limitations of bcr/abl translocation probes and that FISH interphase signals should be confirmed on metaphase spreads for accurate diagnosis.